[2022-11-30 17:00:13,928 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.21.5, tag: Nephele_2022_October_06, commit: c1eb66c [2022-11-30 17:00:13,928 - INFO] Python version: 3.8.13 [2022-11-30 17:00:13,928 - INFO] Current time: 2022-11-30 17:00 [2022-11-30 17:00:13,928 - INFO] Pipeline name: QC Reads [2022-11-30 17:00:14,180 - INFO] Job Description: Arch-v56-B_221130 [2022-11-30 17:00:14,180 - INFO] Job parameters job_id: 1c437ddc2cca inputs_dir: None outputs_dir: None map_file: <_io.TextIOWrapper name='/nephele_data/inputs/Arch-v56-B_Nephele-metadata_corrected.txt' mode='r' encoding='UTF-8'> data_type: PE run_cutadapt: False error_rate: 0.1 indels: True overlap: 3 match_read_wildcards: True match_adapter_wildcards: True adapter_f: None adapter_r: None front_f: None front_r: None anywhere_f: None anywhere_r: None run_qual_trimming: True window_size: 4 req_qual: 12 lead_qual: 3 trail_qual: 3 minlen: 30 avg_qual: 0 run_flash2_merge: True f2_min_overlap: 10 f2_max_overlap: 315 f2_min_overlap_outie: 35 f2_max_mismatch_density: 0.25 [2022-11-30 17:00:14,180 - INFO] Checking Mapfile for Gzipped inputs. [2022-11-30 17:00:14,181 - INFO] Gzipped files listed in map file, attempting to rm .gz extension. [2022-11-30 17:00:14,181 - INFO] Done. Attempting file decompression. [2022-11-30 17:00:49,282 - INFO] Finished decompression. [2022-11-30 17:00:49,282 - INFO] Starting pipe... [2022-11-30 17:00:49,291 - INFO] Trying to generate samples [2022-11-30 17:00:49,291 - INFO] Starting Fastqc, outputs in /nephele_data/outputs/multiqc_input/. [2022-11-30 17:00:49,292 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW01trimB_R1.fq [2022-11-30 17:00:53,760 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW01trimB_R2.fq [2022-11-30 17:00:56,992 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW02trimB_R1.fq [2022-11-30 17:01:00,223 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW02trimB_R2.fq [2022-11-30 17:01:03,479 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW03trimB_R1.fq [2022-11-30 17:01:06,720 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW03trimB_R2.fq [2022-11-30 17:01:09,957 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW04trimB_R1.fq [2022-11-30 17:01:14,189 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW04trimB_R2.fq [2022-11-30 17:01:17,421 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW05trimB_R1.fq [2022-11-30 17:01:20,657 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW05trimB_R2.fq [2022-11-30 17:01:23,893 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW06trimB_R1.fq [2022-11-30 17:01:27,124 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW06trimB_R2.fq [2022-11-30 17:01:30,406 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW07trimB_R1.fq [2022-11-30 17:01:34,635 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW07trimB_R2.fq [2022-11-30 17:01:38,869 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW08trimB_R1.fq [2022-11-30 17:01:42,099 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW08trimB_R2.fq [2022-11-30 17:01:45,392 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW09trimB_R1.fq [2022-11-30 17:01:48,630 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW09trimB_R2.fq [2022-11-30 17:01:51,894 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW10trimB_R1.fq [2022-11-30 17:01:55,165 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW10trimB_R2.fq [2022-11-30 17:01:58,399 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW11trimB_R1.fq [2022-11-30 17:02:01,632 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW11trimB_R2.fq [2022-11-30 17:02:04,871 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW12trimB_R1.fq [2022-11-30 17:02:08,111 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW12trimB_R2.fq [2022-11-30 17:02:11,344 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW13trimB_R1.fq [2022-11-30 17:02:15,629 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW13trimB_R2.fq [2022-11-30 17:02:18,864 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW14trimB_R1.fq [2022-11-30 17:02:22,097 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW14trimB_R2.fq [2022-11-30 17:02:25,335 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW15trimB_R1.fq [2022-11-30 17:02:28,569 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW15trimB_R2.fq [2022-11-30 17:02:31,804 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW16trimB_R1.fq [2022-11-30 17:02:35,097 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW16trimB_R2.fq [2022-11-30 17:02:38,331 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW17trimB_R1.fq [2022-11-30 17:02:42,570 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW17trimB_R2.fq [2022-11-30 17:02:45,811 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW18trimB_R1.fq [2022-11-30 17:02:49,047 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW18trimB_R2.fq [2022-11-30 17:02:52,289 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW19trimB_R1.fq [2022-11-30 17:02:55,523 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW19trimB_R2.fq [2022-11-30 17:02:58,785 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW20trimB_R1.fq [2022-11-30 17:03:02,014 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW20trimB_R2.fq [2022-11-30 17:03:05,248 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW21trimB_R1.fq [2022-11-30 17:03:08,491 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW21trimB_R2.fq [2022-11-30 17:03:11,729 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW22trimB_R1.fq [2022-11-30 17:03:14,964 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW22trimB_R2.fq [2022-11-30 17:03:18,196 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW23trimB_R1.fq [2022-11-30 17:03:22,432 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW23trimB_R2.fq [2022-11-30 17:03:25,669 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW24trimB_R1.fq [2022-11-30 17:03:28,904 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW24trimB_R2.fq [2022-11-30 17:03:32,149 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW25trimB_R1.fq [2022-11-30 17:03:35,385 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW25trimB_R2.fq [2022-11-30 17:03:38,620 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW26trimB_R1.fq [2022-11-30 17:03:41,855 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW26trimB_R2.fq [2022-11-30 17:03:45,112 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW27trimB_R1.fq [2022-11-30 17:03:48,350 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW27trimB_R2.fq [2022-11-30 17:03:51,587 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW28trimB_R1.fq [2022-11-30 17:03:54,820 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW28trimB_R2.fq [2022-11-30 17:03:58,130 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW29trimB_R1.fq [2022-11-30 17:04:01,370 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW29trimB_R2.fq [2022-11-30 17:04:04,605 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW30trimB_R1.fq [2022-11-30 17:04:07,845 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW30trimB_R2.fq [2022-11-30 17:04:11,107 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW31trimB_R1.fq [2022-11-30 17:04:14,420 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW31trimB_R2.fq [2022-11-30 17:04:17,655 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW32trimB_R1.fq [2022-11-30 17:04:20,896 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW32trimB_R2.fq [2022-11-30 17:04:24,128 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW33trimB_R1.fq [2022-11-30 17:04:27,376 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW33trimB_R2.fq [2022-11-30 17:04:30,610 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW34trimB_R1.fq [2022-11-30 17:04:33,857 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW34trimB_R2.fq [2022-11-30 17:04:37,096 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW35trimB_R1.fq [2022-11-30 17:04:40,335 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW35trimB_R2.fq [2022-11-30 17:04:43,593 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW36trimB_R1.fq [2022-11-30 17:04:46,825 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW36trimB_R2.fq [2022-11-30 17:04:50,057 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW37trimB_R1.fq [2022-11-30 17:04:52,297 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW37trimB_R2.fq [2022-11-30 17:04:54,538 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW38trimB_R1.fq [2022-11-30 17:04:56,771 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW38trimB_R2.fq [2022-11-30 17:04:59,008 - INFO] Finished Fastqc, see /nephele_data/outputs/multiqc_input/ for outputs. [2022-11-30 17:04:59,008 - INFO] Run Trimmomatic quality trimming selected. [2022-11-30 17:04:59,008 - INFO] Trying to create /nephele_data/outputs/qtrimmed_seqs/. [2022-11-30 17:04:59,018 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW01trimB_R1.fq /nephele_data/inputs/4061-JW01trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW01trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:05,023 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW01trimB_R1.fq /nephele_data/inputs/4061-JW01trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW01trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW01trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimB_2U.fastq.gz Input Read Pairs: 148632 Both Surviving: 148626 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:05,023 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW02trimB_R1.fq /nephele_data/inputs/4061-JW02trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW02trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:11,548 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW02trimB_R1.fq /nephele_data/inputs/4061-JW02trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW02trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW02trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimB_2U.fastq.gz Input Read Pairs: 169030 Both Surviving: 169023 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:11,548 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW03trimB_R1.fq /nephele_data/inputs/4061-JW03trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW03trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:17,957 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW03trimB_R1.fq /nephele_data/inputs/4061-JW03trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW03trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW03trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimB_2U.fastq.gz Input Read Pairs: 150917 Both Surviving: 150909 (99.99%) Forward Only Surviving: 8 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:17,957 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW04trimB_R1.fq /nephele_data/inputs/4061-JW04trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW04trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:22,342 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW04trimB_R1.fq /nephele_data/inputs/4061-JW04trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW04trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW04trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimB_2U.fastq.gz Input Read Pairs: 93207 Both Surviving: 93198 (99.99%) Forward Only Surviving: 9 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:22,342 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW05trimB_R1.fq /nephele_data/inputs/4061-JW05trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW05trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:27,949 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW05trimB_R1.fq /nephele_data/inputs/4061-JW05trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW05trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW05trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimB_2U.fastq.gz Input Read Pairs: 146784 Both Surviving: 146773 (99.99%) Forward Only Surviving: 11 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:27,949 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW06trimB_R1.fq /nephele_data/inputs/4061-JW06trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW06trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:34,994 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW06trimB_R1.fq /nephele_data/inputs/4061-JW06trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW06trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW06trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimB_2U.fastq.gz Input Read Pairs: 192443 Both Surviving: 192435 (100.00%) Forward Only Surviving: 8 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:34,994 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW07trimB_R1.fq /nephele_data/inputs/4061-JW07trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW07trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:42,884 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW07trimB_R1.fq /nephele_data/inputs/4061-JW07trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW07trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW07trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimB_2U.fastq.gz Input Read Pairs: 216726 Both Surviving: 216716 (100.00%) Forward Only Surviving: 10 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:42,884 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW08trimB_R1.fq /nephele_data/inputs/4061-JW08trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW08trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:49,090 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW08trimB_R1.fq /nephele_data/inputs/4061-JW08trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW08trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW08trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimB_2U.fastq.gz Input Read Pairs: 149974 Both Surviving: 149961 (99.99%) Forward Only Surviving: 13 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:49,091 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW09trimB_R1.fq /nephele_data/inputs/4061-JW09trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW09trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:55,577 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW09trimB_R1.fq /nephele_data/inputs/4061-JW09trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW09trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW09trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimB_2U.fastq.gz Input Read Pairs: 170074 Both Surviving: 170072 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:55,577 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW10trimB_R1.fq /nephele_data/inputs/4061-JW10trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW10trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:00,744 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW10trimB_R1.fq /nephele_data/inputs/4061-JW10trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW10trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW10trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimB_2U.fastq.gz Input Read Pairs: 117772 Both Surviving: 117765 (99.99%) Forward Only Surviving: 7 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:00,744 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW11trimB_R1.fq /nephele_data/inputs/4061-JW11trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW11trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:06,638 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW11trimB_R1.fq /nephele_data/inputs/4061-JW11trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW11trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW11trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimB_2U.fastq.gz Input Read Pairs: 143846 Both Surviving: 143843 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:06,638 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW12trimB_R1.fq /nephele_data/inputs/4061-JW12trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW12trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:10,225 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW12trimB_R1.fq /nephele_data/inputs/4061-JW12trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW12trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW12trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimB_2U.fastq.gz Input Read Pairs: 74630 Both Surviving: 74626 (99.99%) Forward Only Surviving: 4 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:10,225 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW13trimB_R1.fq /nephele_data/inputs/4061-JW13trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW13trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:16,122 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW13trimB_R1.fq /nephele_data/inputs/4061-JW13trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW13trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW13trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimB_2U.fastq.gz Input Read Pairs: 145151 Both Surviving: 145147 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:16,122 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW14trimB_R1.fq /nephele_data/inputs/4061-JW14trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW14trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:20,924 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW14trimB_R1.fq /nephele_data/inputs/4061-JW14trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW14trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW14trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimB_2U.fastq.gz Input Read Pairs: 112771 Both Surviving: 112759 (99.99%) Forward Only Surviving: 12 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:20,924 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW15trimB_R1.fq /nephele_data/inputs/4061-JW15trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW15trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:26,033 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW15trimB_R1.fq /nephele_data/inputs/4061-JW15trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW15trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW15trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimB_2U.fastq.gz Input Read Pairs: 129727 Both Surviving: 129721 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:26,033 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW16trimB_R1.fq /nephele_data/inputs/4061-JW16trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW16trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:31,276 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW16trimB_R1.fq /nephele_data/inputs/4061-JW16trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW16trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW16trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimB_2U.fastq.gz Input Read Pairs: 123572 Both Surviving: 123565 (99.99%) Forward Only Surviving: 7 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:31,276 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW17trimB_R1.fq /nephele_data/inputs/4061-JW17trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW17trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:38,649 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW17trimB_R1.fq /nephele_data/inputs/4061-JW17trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW17trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW17trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimB_2U.fastq.gz Input Read Pairs: 191165 Both Surviving: 191150 (99.99%) Forward Only Surviving: 15 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:38,649 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW18trimB_R1.fq /nephele_data/inputs/4061-JW18trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW18trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:46,151 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW18trimB_R1.fq /nephele_data/inputs/4061-JW18trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW18trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW18trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimB_2U.fastq.gz Input Read Pairs: 189420 Both Surviving: 189412 (100.00%) Forward Only Surviving: 8 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:46,151 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW19trimB_R1.fq /nephele_data/inputs/4061-JW19trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW19trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:52,211 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW19trimB_R1.fq /nephele_data/inputs/4061-JW19trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW19trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW19trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimB_2U.fastq.gz Input Read Pairs: 138846 Both Surviving: 138841 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:52,211 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW20trimB_R1.fq /nephele_data/inputs/4061-JW20trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW20trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:57,460 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW20trimB_R1.fq /nephele_data/inputs/4061-JW20trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW20trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW20trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimB_2U.fastq.gz Input Read Pairs: 125643 Both Surviving: 125639 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:57,460 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW21trimB_R1.fq /nephele_data/inputs/4061-JW21trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW21trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:01,503 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW21trimB_R1.fq /nephele_data/inputs/4061-JW21trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW21trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW21trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimB_2U.fastq.gz Input Read Pairs: 91330 Both Surviving: 91330 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:01,504 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW22trimB_R1.fq /nephele_data/inputs/4061-JW22trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW22trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:07,222 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW22trimB_R1.fq /nephele_data/inputs/4061-JW22trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW22trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW22trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimB_2U.fastq.gz Input Read Pairs: 141421 Both Surviving: 141414 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:07,223 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW23trimB_R1.fq /nephele_data/inputs/4061-JW23trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW23trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:12,160 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW23trimB_R1.fq /nephele_data/inputs/4061-JW23trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW23trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW23trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimB_2U.fastq.gz Input Read Pairs: 116353 Both Surviving: 116348 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:12,160 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW24trimB_R1.fq /nephele_data/inputs/4061-JW24trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW24trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:16,783 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW24trimB_R1.fq /nephele_data/inputs/4061-JW24trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW24trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW24trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimB_2U.fastq.gz Input Read Pairs: 117607 Both Surviving: 117606 (100.00%) Forward Only Surviving: 1 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:16,783 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW25trimB_R1.fq /nephele_data/inputs/4061-JW25trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW25trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:21,387 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW25trimB_R1.fq /nephele_data/inputs/4061-JW25trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW25trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW25trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimB_2U.fastq.gz Input Read Pairs: 100449 Both Surviving: 100446 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:21,388 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW26trimB_R1.fq /nephele_data/inputs/4061-JW26trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW26trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:27,812 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW26trimB_R1.fq /nephele_data/inputs/4061-JW26trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW26trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW26trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimB_2U.fastq.gz Input Read Pairs: 162051 Both Surviving: 162039 (99.99%) Forward Only Surviving: 12 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:27,812 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW27trimB_R1.fq /nephele_data/inputs/4061-JW27trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW27trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:33,861 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW27trimB_R1.fq /nephele_data/inputs/4061-JW27trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW27trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW27trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimB_2U.fastq.gz Input Read Pairs: 149568 Both Surviving: 149560 (99.99%) Forward Only Surviving: 8 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:33,861 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW28trimB_R1.fq /nephele_data/inputs/4061-JW28trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW28trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:39,184 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW28trimB_R1.fq /nephele_data/inputs/4061-JW28trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW28trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW28trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimB_2U.fastq.gz Input Read Pairs: 127958 Both Surviving: 127954 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:39,184 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW29trimB_R1.fq /nephele_data/inputs/4061-JW29trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW29trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:45,100 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW29trimB_R1.fq /nephele_data/inputs/4061-JW29trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW29trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW29trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimB_2U.fastq.gz Input Read Pairs: 147289 Both Surviving: 147285 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:45,100 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW30trimB_R1.fq /nephele_data/inputs/4061-JW30trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW30trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:50,272 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW30trimB_R1.fq /nephele_data/inputs/4061-JW30trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW30trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW30trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimB_2U.fastq.gz Input Read Pairs: 123978 Both Surviving: 123976 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:50,272 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW31trimB_R1.fq /nephele_data/inputs/4061-JW31trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW31trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:54,485 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW31trimB_R1.fq /nephele_data/inputs/4061-JW31trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW31trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW31trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimB_2U.fastq.gz Input Read Pairs: 90504 Both Surviving: 90502 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:54,485 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW32trimB_R1.fq /nephele_data/inputs/4061-JW32trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW32trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:00,270 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW32trimB_R1.fq /nephele_data/inputs/4061-JW32trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW32trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW32trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimB_2U.fastq.gz Input Read Pairs: 147458 Both Surviving: 147448 (99.99%) Forward Only Surviving: 10 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:00,270 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW33trimB_R1.fq /nephele_data/inputs/4061-JW33trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW33trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:03,634 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW33trimB_R1.fq /nephele_data/inputs/4061-JW33trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW33trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW33trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimB_2U.fastq.gz Input Read Pairs: 68956 Both Surviving: 68952 (99.99%) Forward Only Surviving: 4 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:03,634 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW34trimB_R1.fq /nephele_data/inputs/4061-JW34trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW34trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:09,792 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW34trimB_R1.fq /nephele_data/inputs/4061-JW34trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW34trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW34trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimB_2U.fastq.gz Input Read Pairs: 149611 Both Surviving: 149605 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:09,792 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW35trimB_R1.fq /nephele_data/inputs/4061-JW35trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW35trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:14,882 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW35trimB_R1.fq /nephele_data/inputs/4061-JW35trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW35trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW35trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimB_2U.fastq.gz Input Read Pairs: 126027 Both Surviving: 126024 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:14,882 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW36trimB_R1.fq /nephele_data/inputs/4061-JW36trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW36trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:18,684 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW36trimB_R1.fq /nephele_data/inputs/4061-JW36trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW36trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW36trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimB_2U.fastq.gz Input Read Pairs: 85762 Both Surviving: 85760 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:18,684 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW37trimB_R1.fq /nephele_data/inputs/4061-JW37trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW37trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:18,902 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW37trimB_R1.fq /nephele_data/inputs/4061-JW37trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW37trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW37trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimB_2U.fastq.gz Input Read Pairs: 196 Both Surviving: 196 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:18,903 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW38trimB_R1.fq /nephele_data/inputs/4061-JW38trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW38trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:08:19,115 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW38trimB_R1.fq /nephele_data/inputs/4061-JW38trimB_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW38trimB.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW38trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimB_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimB_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimB_2U.fastq.gz Input Read Pairs: 137 Both Surviving: 137 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:08:19,115 - INFO] Quality trimming complete, see /nephele_data/outputs/multiqc_input/trimmo.log. [2022-11-30 17:08:19,115 - INFO] Run paired end merging selected. [2022-11-30 17:08:19,125 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW01trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW01trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimB_2P.fastq.gz [2022-11-30 17:08:24,869 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW01trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW01trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW01trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW01trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 148626 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 148626 [FLASH] Combined pairs: 144466 [FLASH] Innie pairs: 144263 (99.86% of combined) [FLASH] Outie pairs: 203 (0.14% of combined) [FLASH] Uncombined pairs: 4160 [FLASH] Percent combined: 97.20% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.733 seconds elapsed [2022-11-30 17:08:24,869 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW02trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW02trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimB_2P.fastq.gz [2022-11-30 17:08:30,908 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW02trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW02trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW02trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW02trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 169023 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 169023 [FLASH] Combined pairs: 166018 [FLASH] Innie pairs: 163687 (98.60% of combined) [FLASH] Outie pairs: 2331 (1.40% of combined) [FLASH] Uncombined pairs: 3005 [FLASH] Percent combined: 98.22% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.028 seconds elapsed [2022-11-30 17:08:30,908 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW03trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW03trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimB_2P.fastq.gz [2022-11-30 17:08:36,931 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW03trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW03trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW03trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW03trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 150909 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 150909 [FLASH] Combined pairs: 146603 [FLASH] Innie pairs: 144702 (98.70% of combined) [FLASH] Outie pairs: 1901 (1.30% of combined) [FLASH] Uncombined pairs: 4306 [FLASH] Percent combined: 97.15% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.012 seconds elapsed [2022-11-30 17:08:36,931 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW04trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW04trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimB_2P.fastq.gz [2022-11-30 17:08:41,067 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW04trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW04trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW04trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW04trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 93198 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 93198 [FLASH] Combined pairs: 89342 [FLASH] Innie pairs: 88084 (98.59% of combined) [FLASH] Outie pairs: 1258 (1.41% of combined) [FLASH] Uncombined pairs: 3856 [FLASH] Percent combined: 95.86% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.126 seconds elapsed [2022-11-30 17:08:41,067 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW05trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW05trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimB_2P.fastq.gz [2022-11-30 17:08:46,085 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW05trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW05trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW05trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW05trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 146773 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 146773 [FLASH] Combined pairs: 143750 [FLASH] Innie pairs: 141865 (98.69% of combined) [FLASH] Outie pairs: 1885 (1.31% of combined) [FLASH] Uncombined pairs: 3023 [FLASH] Percent combined: 97.94% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.007 seconds elapsed [2022-11-30 17:08:46,085 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW06trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW06trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimB_2P.fastq.gz [2022-11-30 17:08:52,717 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW06trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW06trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW06trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW06trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 192435 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 192435 [FLASH] Combined pairs: 189182 [FLASH] Innie pairs: 186196 (98.42% of combined) [FLASH] Outie pairs: 2986 (1.58% of combined) [FLASH] Uncombined pairs: 3253 [FLASH] Percent combined: 98.31% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.621 seconds elapsed [2022-11-30 17:08:52,717 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW07trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW07trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimB_2P.fastq.gz [2022-11-30 17:09:00,167 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW07trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW07trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW07trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW07trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 216716 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 216716 [FLASH] Combined pairs: 213348 [FLASH] Innie pairs: 210857 (98.83% of combined) [FLASH] Outie pairs: 2491 (1.17% of combined) [FLASH] Uncombined pairs: 3368 [FLASH] Percent combined: 98.45% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.439 seconds elapsed [2022-11-30 17:09:00,167 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW08trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW08trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimB_2P.fastq.gz [2022-11-30 17:09:05,888 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW08trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW08trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW08trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW08trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 149961 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 149961 [FLASH] Combined pairs: 144951 [FLASH] Innie pairs: 144758 (99.87% of combined) [FLASH] Outie pairs: 193 (0.13% of combined) [FLASH] Uncombined pairs: 5010 [FLASH] Percent combined: 96.66% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.710 seconds elapsed [2022-11-30 17:09:05,888 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW09trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW09trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimB_2P.fastq.gz [2022-11-30 17:09:11,906 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW09trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW09trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW09trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW09trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 170072 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 170072 [FLASH] Combined pairs: 166973 [FLASH] Innie pairs: 164635 (98.60% of combined) [FLASH] Outie pairs: 2338 (1.40% of combined) [FLASH] Uncombined pairs: 3099 [FLASH] Percent combined: 98.18% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.007 seconds elapsed [2022-11-30 17:09:11,906 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW10trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW10trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimB_2P.fastq.gz [2022-11-30 17:09:16,786 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW10trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW10trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW10trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW10trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 117765 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 117765 [FLASH] Combined pairs: 114000 [FLASH] Innie pairs: 112652 (98.82% of combined) [FLASH] Outie pairs: 1348 (1.18% of combined) [FLASH] Uncombined pairs: 3765 [FLASH] Percent combined: 96.80% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.869 seconds elapsed [2022-11-30 17:09:16,786 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW11trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW11trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimB_2P.fastq.gz [2022-11-30 17:09:22,233 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW11trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW11trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW11trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW11trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 143843 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 143843 [FLASH] Combined pairs: 140276 [FLASH] Innie pairs: 137950 (98.34% of combined) [FLASH] Outie pairs: 2326 (1.66% of combined) [FLASH] Uncombined pairs: 3567 [FLASH] Percent combined: 97.52% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.437 seconds elapsed [2022-11-30 17:09:22,234 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW12trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW12trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimB_2P.fastq.gz [2022-11-30 17:09:25,546 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW12trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW12trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW12trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW12trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 74626 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 74626 [FLASH] Combined pairs: 71920 [FLASH] Innie pairs: 70576 (98.13% of combined) [FLASH] Outie pairs: 1344 (1.87% of combined) [FLASH] Uncombined pairs: 2706 [FLASH] Percent combined: 96.37% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.301 seconds elapsed [2022-11-30 17:09:25,546 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW13trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW13trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimB_2P.fastq.gz [2022-11-30 17:09:31,079 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW13trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW13trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW13trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW13trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 145147 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 145147 [FLASH] Combined pairs: 141208 [FLASH] Innie pairs: 140931 (99.80% of combined) [FLASH] Outie pairs: 277 (0.20% of combined) [FLASH] Uncombined pairs: 3939 [FLASH] Percent combined: 97.29% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.523 seconds elapsed [2022-11-30 17:09:31,079 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW14trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW14trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimB_2P.fastq.gz [2022-11-30 17:09:35,401 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW14trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW14trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW14trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW14trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 112759 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 112759 [FLASH] Combined pairs: 109770 [FLASH] Innie pairs: 108366 (98.72% of combined) [FLASH] Outie pairs: 1404 (1.28% of combined) [FLASH] Uncombined pairs: 2989 [FLASH] Percent combined: 97.35% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.311 seconds elapsed [2022-11-30 17:09:35,401 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW15trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW15trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimB_2P.fastq.gz [2022-11-30 17:09:40,233 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW15trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW15trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW15trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW15trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 129721 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 129721 [FLASH] Combined pairs: 127016 [FLASH] Innie pairs: 125485 (98.79% of combined) [FLASH] Outie pairs: 1531 (1.21% of combined) [FLASH] Uncombined pairs: 2705 [FLASH] Percent combined: 97.91% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.821 seconds elapsed [2022-11-30 17:09:40,233 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW16trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW16trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimB_2P.fastq.gz [2022-11-30 17:09:45,013 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW16trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW16trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW16trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW16trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 123565 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 123565 [FLASH] Combined pairs: 120679 [FLASH] Innie pairs: 119177 (98.76% of combined) [FLASH] Outie pairs: 1502 (1.24% of combined) [FLASH] Uncombined pairs: 2886 [FLASH] Percent combined: 97.66% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.769 seconds elapsed [2022-11-30 17:09:45,013 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW17trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW17trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimB_2P.fastq.gz [2022-11-30 17:09:51,961 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW17trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW17trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW17trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW17trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 191150 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 191150 [FLASH] Combined pairs: 187572 [FLASH] Innie pairs: 185133 (98.70% of combined) [FLASH] Outie pairs: 2439 (1.30% of combined) [FLASH] Uncombined pairs: 3578 [FLASH] Percent combined: 98.13% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.937 seconds elapsed [2022-11-30 17:09:51,961 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW18trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW18trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimB_2P.fastq.gz [2022-11-30 17:09:59,180 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW18trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW18trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW18trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW18trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 189412 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 189412 [FLASH] Combined pairs: 185326 [FLASH] Innie pairs: 182581 (98.52% of combined) [FLASH] Outie pairs: 2745 (1.48% of combined) [FLASH] Uncombined pairs: 4086 [FLASH] Percent combined: 97.84% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.209 seconds elapsed [2022-11-30 17:09:59,180 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW19trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW19trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimB_2P.fastq.gz [2022-11-30 17:10:04,705 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW19trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW19trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW19trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW19trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 138841 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 138841 [FLASH] Combined pairs: 133684 [FLASH] Innie pairs: 123378 (92.29% of combined) [FLASH] Outie pairs: 10306 (7.71% of combined) [FLASH] Uncombined pairs: 5157 [FLASH] Percent combined: 96.29% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.514 seconds elapsed [2022-11-30 17:10:04,705 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW20trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW20trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimB_2P.fastq.gz [2022-11-30 17:10:09,654 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW20trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW20trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW20trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW20trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 125639 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 125639 [FLASH] Combined pairs: 121192 [FLASH] Innie pairs: 118908 (98.12% of combined) [FLASH] Outie pairs: 2284 (1.88% of combined) [FLASH] Uncombined pairs: 4447 [FLASH] Percent combined: 96.46% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.938 seconds elapsed [2022-11-30 17:10:09,654 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW21trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW21trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimB_2P.fastq.gz [2022-11-30 17:10:13,262 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW21trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW21trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW21trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW21trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 91330 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 91330 [FLASH] Combined pairs: 87708 [FLASH] Innie pairs: 86273 (98.36% of combined) [FLASH] Outie pairs: 1435 (1.64% of combined) [FLASH] Uncombined pairs: 3622 [FLASH] Percent combined: 96.03% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.597 seconds elapsed [2022-11-30 17:10:13,262 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW22trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW22trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimB_2P.fastq.gz [2022-11-30 17:10:18,498 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW22trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW22trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW22trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW22trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 141414 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 141414 [FLASH] Combined pairs: 137997 [FLASH] Innie pairs: 136293 (98.77% of combined) [FLASH] Outie pairs: 1704 (1.23% of combined) [FLASH] Uncombined pairs: 3417 [FLASH] Percent combined: 97.58% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.225 seconds elapsed [2022-11-30 17:10:18,498 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW23trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW23trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimB_2P.fastq.gz [2022-11-30 17:10:22,964 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW23trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW23trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW23trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW23trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 116348 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 116348 [FLASH] Combined pairs: 113544 [FLASH] Innie pairs: 111541 (98.24% of combined) [FLASH] Outie pairs: 2003 (1.76% of combined) [FLASH] Uncombined pairs: 2804 [FLASH] Percent combined: 97.59% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.456 seconds elapsed [2022-11-30 17:10:22,965 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW24trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW24trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimB_2P.fastq.gz [2022-11-30 17:10:27,431 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW24trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW24trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW24trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW24trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 117606 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 117606 [FLASH] Combined pairs: 115330 [FLASH] Innie pairs: 113878 (98.74% of combined) [FLASH] Outie pairs: 1452 (1.26% of combined) [FLASH] Uncombined pairs: 2276 [FLASH] Percent combined: 98.06% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.456 seconds elapsed [2022-11-30 17:10:27,431 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW25trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW25trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimB_2P.fastq.gz [2022-11-30 17:10:31,482 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW25trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW25trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW25trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW25trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 100446 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 100446 [FLASH] Combined pairs: 96484 [FLASH] Innie pairs: 90859 (94.17% of combined) [FLASH] Outie pairs: 5625 (5.83% of combined) [FLASH] Uncombined pairs: 3962 [FLASH] Percent combined: 96.06% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.041 seconds elapsed [2022-11-30 17:10:31,483 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW26trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW26trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimB_2P.fastq.gz [2022-11-30 17:10:37,478 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW26trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW26trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW26trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW26trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 162039 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 162039 [FLASH] Combined pairs: 158541 [FLASH] Innie pairs: 156157 (98.50% of combined) [FLASH] Outie pairs: 2384 (1.50% of combined) [FLASH] Uncombined pairs: 3498 [FLASH] Percent combined: 97.84% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.984 seconds elapsed [2022-11-30 17:10:37,478 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW27trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW27trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimB_2P.fastq.gz [2022-11-30 17:10:43,084 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW27trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW27trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW27trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW27trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 149560 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 149560 [FLASH] Combined pairs: 146413 [FLASH] Innie pairs: 144088 (98.41% of combined) [FLASH] Outie pairs: 2325 (1.59% of combined) [FLASH] Uncombined pairs: 3147 [FLASH] Percent combined: 97.90% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.595 seconds elapsed [2022-11-30 17:10:43,084 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW28trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW28trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimB_2P.fastq.gz [2022-11-30 17:10:48,239 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW28trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW28trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW28trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW28trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 127954 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 127954 [FLASH] Combined pairs: 123817 [FLASH] Innie pairs: 121832 (98.40% of combined) [FLASH] Outie pairs: 1985 (1.60% of combined) [FLASH] Uncombined pairs: 4137 [FLASH] Percent combined: 96.77% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.144 seconds elapsed [2022-11-30 17:10:48,239 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW29trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW29trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimB_2P.fastq.gz [2022-11-30 17:10:53,723 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW29trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW29trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW29trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW29trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 147285 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 147285 [FLASH] Combined pairs: 144473 [FLASH] Innie pairs: 142161 (98.40% of combined) [FLASH] Outie pairs: 2312 (1.60% of combined) [FLASH] Uncombined pairs: 2812 [FLASH] Percent combined: 98.09% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.473 seconds elapsed [2022-11-30 17:10:53,723 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW30trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW30trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimB_2P.fastq.gz [2022-11-30 17:10:58,493 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW30trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW30trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW30trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW30trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 123976 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 123976 [FLASH] Combined pairs: 120818 [FLASH] Innie pairs: 119110 (98.59% of combined) [FLASH] Outie pairs: 1708 (1.41% of combined) [FLASH] Uncombined pairs: 3158 [FLASH] Percent combined: 97.45% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.759 seconds elapsed [2022-11-30 17:10:58,493 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW31trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW31trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimB_2P.fastq.gz [2022-11-30 17:11:02,282 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW31trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW31trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW31trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW31trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 90502 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 90502 [FLASH] Combined pairs: 87216 [FLASH] Innie pairs: 85657 (98.21% of combined) [FLASH] Outie pairs: 1559 (1.79% of combined) [FLASH] Uncombined pairs: 3286 [FLASH] Percent combined: 96.37% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.780 seconds elapsed [2022-11-30 17:11:02,283 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW32trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW32trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimB_2P.fastq.gz [2022-11-30 17:11:07,625 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW32trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW32trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW32trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW32trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 147448 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 147448 [FLASH] Combined pairs: 144710 [FLASH] Innie pairs: 142775 (98.66% of combined) [FLASH] Outie pairs: 1935 (1.34% of combined) [FLASH] Uncombined pairs: 2738 [FLASH] Percent combined: 98.14% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.331 seconds elapsed [2022-11-30 17:11:07,625 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW33trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW33trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimB_2P.fastq.gz [2022-11-30 17:11:10,576 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW33trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW33trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW33trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW33trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 68952 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 68952 [FLASH] Combined pairs: 66367 [FLASH] Innie pairs: 65614 (98.87% of combined) [FLASH] Outie pairs: 753 (1.13% of combined) [FLASH] Uncombined pairs: 2585 [FLASH] Percent combined: 96.25% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 2.940 seconds elapsed [2022-11-30 17:11:10,576 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW34trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW34trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimB_2P.fastq.gz [2022-11-30 17:11:16,423 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW34trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW34trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW34trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW34trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 149605 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 149605 [FLASH] Combined pairs: 146734 [FLASH] Innie pairs: 144764 (98.66% of combined) [FLASH] Outie pairs: 1970 (1.34% of combined) [FLASH] Uncombined pairs: 2871 [FLASH] Percent combined: 98.08% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.837 seconds elapsed [2022-11-30 17:11:16,424 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW35trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW35trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimB_2P.fastq.gz [2022-11-30 17:11:21,073 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW35trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW35trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW35trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW35trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 126024 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 126024 [FLASH] Combined pairs: 123287 [FLASH] Innie pairs: 121588 (98.62% of combined) [FLASH] Outie pairs: 1699 (1.38% of combined) [FLASH] Uncombined pairs: 2737 [FLASH] Percent combined: 97.83% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.638 seconds elapsed [2022-11-30 17:11:21,073 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW36trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW36trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimB_2P.fastq.gz [2022-11-30 17:11:24,635 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW36trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW36trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW36trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW36trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 85760 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 85760 [FLASH] Combined pairs: 82791 [FLASH] Innie pairs: 81510 (98.45% of combined) [FLASH] Outie pairs: 1281 (1.55% of combined) [FLASH] Uncombined pairs: 2969 [FLASH] Percent combined: 96.54% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.552 seconds elapsed [2022-11-30 17:11:24,636 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW37trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW37trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimB_2P.fastq.gz [2022-11-30 17:11:24,665 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW37trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW37trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW37trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW37trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 196 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 196 [FLASH] Combined pairs: 5 [FLASH] Innie pairs: 4 (80.00% of combined) [FLASH] Outie pairs: 1 (20.00% of combined) [FLASH] Uncombined pairs: 191 [FLASH] Percent combined: 2.55% [FLASH] [FLASH] Writing histogram files. [FLASH] WARNING: An unexpectedly high proportion of combined pairs (20.00%) overlapped by more than 315 bp, the --max-overlap (-M) parameter. Consider increasing this parameter. (As-is, FLASH is penalizing overlaps longer than 315 bp when considering them for possible combining!) [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 0.020 seconds elapsed [FLASH] Finished with 1 warning (see above) [2022-11-30 17:11:24,665 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW38trimB_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW38trimB_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimB_2P.fastq.gz [2022-11-30 17:11:24,690 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW38trimB_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW38trimB_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW38trimB_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimB_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimB_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimB_merged.hist [FLASH] /nephele_data/outputs/merged//JW38trimB_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 137 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 137 [FLASH] Combined pairs: 1 [FLASH] Innie pairs: 1 (100.00% of combined) [FLASH] Outie pairs: 0 (0.00% of combined) [FLASH] Uncombined pairs: 136 [FLASH] Percent combined: 0.73% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 0.017 seconds elapsed [2022-11-30 17:11:24,690 - INFO] Finished paired end merging. [2022-11-30 17:11:24,690 - INFO] Trying to link hist files for multiqc analysis. [2022-11-30 17:11:24,691 - INFO] Finished linking. [2022-11-30 17:11:24,691 - INFO] Trying to run multiqc on /nephele_data/outputs/multiqc_input/. [2022-11-30 17:11:24,691 - INFO] Linking logfile to multiqc inputs directory, /nephele_data/outputs/multiqc_input/. [2022-11-30 17:11:24,692 - INFO] Finished linking. [2022-11-30 17:11:37,421 - INFO] /// MultiQC 🔍 | v1.13.dev0 | multiqc | Report title: Arch-v56-B_221130 | multiqc | Search path : /nephele_data/outputs/multiqc_input | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 191/191 | fastqc | Found 76 reports | trimmomatic | Found 38 logs | flash | Found 38 log reports | flash | Found 38 histogram reports | multiqc | Compressing plot data | multiqc | Report : nephele_data/outputs/Arch-v56-B_221130_multiqc_report.html | multiqc | Data : nephele_data/outputs/Arch-v56-B_221130_multiqc_report_data | multiqc | MultiQC complete [2022-11-30 17:11:37,421 - INFO] Finished multiqc. [2022-11-30 17:11:37,421 - INFO] QC pipeline complete. [2022-11-30 17:11:37,421 - INFO] 0