[2022-11-30 16:59:09,219 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.21.5, tag: Nephele_2022_October_06, commit: c1eb66c [2022-11-30 16:59:09,219 - INFO] Python version: 3.8.13 [2022-11-30 16:59:09,219 - INFO] Current time: 2022-11-30 16:59 [2022-11-30 16:59:09,219 - INFO] Pipeline name: QC Reads [2022-11-30 16:59:09,470 - INFO] Job Description: Ill-v34-R_221130 [2022-11-30 16:59:09,470 - INFO] Job parameters job_id: dab5c109db4c inputs_dir: None outputs_dir: None map_file: <_io.TextIOWrapper name='/nephele_data/inputs/Ill-v34-R_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 16:59:09,470 - INFO] Checking Mapfile for Gzipped inputs. [2022-11-30 16:59:09,471 - INFO] Gzipped files listed in map file, attempting to rm .gz extension. [2022-11-30 16:59:09,471 - INFO] Done. Attempting file decompression. [2022-11-30 16:59:42,806 - INFO] Finished decompression. [2022-11-30 16:59:42,806 - INFO] Starting pipe... [2022-11-30 16:59:42,814 - INFO] Trying to generate samples [2022-11-30 16:59:42,815 - INFO] Starting Fastqc, outputs in /nephele_data/outputs/multiqc_input/. [2022-11-30 16:59:42,815 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW01trimR_R1.fq [2022-11-30 16:59:47,344 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW01trimR_R2.fq [2022-11-30 16:59:50,576 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW02trimR_R1.fq [2022-11-30 16:59:54,809 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW02trimR_R2.fq [2022-11-30 16:59:58,073 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW03trimR_R1.fq [2022-11-30 17:00:01,357 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW03trimR_R2.fq [2022-11-30 17:00:04,590 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW04trimR_R1.fq [2022-11-30 17:00:07,821 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW04trimR_R2.fq [2022-11-30 17:00:11,052 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW05trimR_R1.fq [2022-11-30 17:00:14,283 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW05trimR_R2.fq [2022-11-30 17:00:17,536 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW06trimR_R1.fq [2022-11-30 17:00:20,767 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW06trimR_R2.fq [2022-11-30 17:00:23,999 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW07trimR_R1.fq [2022-11-30 17:00:27,230 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW07trimR_R2.fq [2022-11-30 17:00:30,459 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW08trimR_R1.fq [2022-11-30 17:00:33,706 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW08trimR_R2.fq [2022-11-30 17:00:36,960 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW09trimR_R1.fq [2022-11-30 17:00:40,243 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW09trimR_R2.fq [2022-11-30 17:00:43,475 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW10trimR_R1.fq [2022-11-30 17:00:46,711 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW10trimR_R2.fq [2022-11-30 17:00:49,944 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW11trimR_R1.fq [2022-11-30 17:00:53,245 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW11trimR_R2.fq [2022-11-30 17:00:56,540 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW12trimR_R1.fq [2022-11-30 17:00:59,773 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW12trimR_R2.fq [2022-11-30 17:01:03,005 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW13trimR_R1.fq [2022-11-30 17:01:06,233 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW13trimR_R2.fq [2022-11-30 17:01:09,463 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW14trimR_R1.fq [2022-11-30 17:01:12,695 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW14trimR_R2.fq [2022-11-30 17:01:15,929 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW15trimR_R1.fq [2022-11-30 17:01:19,173 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW15trimR_R2.fq [2022-11-30 17:01:22,407 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW16trimR_R1.fq [2022-11-30 17:01:25,650 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW16trimR_R2.fq [2022-11-30 17:01:28,882 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW17trimR_R1.fq [2022-11-30 17:01:32,143 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW17trimR_R2.fq [2022-11-30 17:01:35,379 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW18trimR_R1.fq [2022-11-30 17:01:38,609 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW18trimR_R2.fq [2022-11-30 17:01:41,841 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW19trimR_R1.fq [2022-11-30 17:01:46,077 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW19trimR_R2.fq [2022-11-30 17:01:49,361 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW20trimR_R1.fq [2022-11-30 17:01:52,592 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW20trimR_R2.fq [2022-11-30 17:01:55,884 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW21trimR_R1.fq [2022-11-30 17:01:59,137 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW21trimR_R2.fq [2022-11-30 17:02:02,368 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW22trimR_R1.fq [2022-11-30 17:02:05,603 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW22trimR_R2.fq [2022-11-30 17:02:08,896 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW23trimR_R1.fq [2022-11-30 17:02:12,131 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW23trimR_R2.fq [2022-11-30 17:02:15,413 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW24trimR_R1.fq [2022-11-30 17:02:18,646 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW24trimR_R2.fq [2022-11-30 17:02:21,878 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW25trimR_R1.fq [2022-11-30 17:02:25,112 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW25trimR_R2.fq [2022-11-30 17:02:28,378 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW26trimR_R1.fq [2022-11-30 17:02:31,641 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW26trimR_R2.fq [2022-11-30 17:02:34,873 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW27trimR_R1.fq [2022-11-30 17:02:38,123 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW27trimR_R2.fq [2022-11-30 17:02:41,417 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW28trimR_R1.fq [2022-11-30 17:02:44,648 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW28trimR_R2.fq [2022-11-30 17:02:48,932 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW29trimR_R1.fq [2022-11-30 17:02:52,169 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW29trimR_R2.fq [2022-11-30 17:02:55,400 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW30trimR_R1.fq [2022-11-30 17:02:59,632 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW30trimR_R2.fq [2022-11-30 17:03:02,907 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW31trimR_R1.fq [2022-11-30 17:03:06,139 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW31trimR_R2.fq [2022-11-30 17:03:09,373 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW32trimR_R1.fq [2022-11-30 17:03:12,645 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW32trimR_R2.fq [2022-11-30 17:03:15,890 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW33trimR_R1.fq [2022-11-30 17:03:19,121 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW33trimR_R2.fq [2022-11-30 17:03:22,351 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW34trimR_R1.fq [2022-11-30 17:03:26,580 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW34trimR_R2.fq [2022-11-30 17:03:29,806 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW35trimR_R1.fq [2022-11-30 17:03:33,034 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW35trimR_R2.fq [2022-11-30 17:03:36,262 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW36trimR_R1.fq [2022-11-30 17:03:39,521 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW36trimR_R2.fq [2022-11-30 17:03:42,748 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW37trimR_R1.fq [2022-11-30 17:03:44,975 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW37trimR_R2.fq [2022-11-30 17:03:47,252 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW38trimR_R1.fq [2022-11-30 17:03:49,474 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW38trimR_R2.fq [2022-11-30 17:03:51,699 - INFO] Finished Fastqc, see /nephele_data/outputs/multiqc_input/ for outputs. [2022-11-30 17:03:51,699 - INFO] Run Trimmomatic quality trimming selected. [2022-11-30 17:03:51,699 - INFO] Trying to create /nephele_data/outputs/qtrimmed_seqs/. [2022-11-30 17:03:51,709 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW01trimR_R1.fq /nephele_data/inputs/4061-JW01trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW01trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:03:56,065 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW01trimR_R1.fq /nephele_data/inputs/4061-JW01trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW01trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW01trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimR_2U.fastq.gz Input Read Pairs: 90422 Both Surviving: 90420 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:03:56,065 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW02trimR_R1.fq /nephele_data/inputs/4061-JW02trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW02trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:00,879 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW02trimR_R1.fq /nephele_data/inputs/4061-JW02trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW02trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW02trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimR_2U.fastq.gz Input Read Pairs: 110176 Both Surviving: 110173 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:00,879 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW03trimR_R1.fq /nephele_data/inputs/4061-JW03trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW03trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:06,806 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW03trimR_R1.fq /nephele_data/inputs/4061-JW03trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW03trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW03trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimR_2U.fastq.gz Input Read Pairs: 146433 Both Surviving: 146429 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:06,806 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW04trimR_R1.fq /nephele_data/inputs/4061-JW04trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW04trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:12,086 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW04trimR_R1.fq /nephele_data/inputs/4061-JW04trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW04trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW04trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimR_2U.fastq.gz Input Read Pairs: 117861 Both Surviving: 117858 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:12,086 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW05trimR_R1.fq /nephele_data/inputs/4061-JW05trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW05trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:16,705 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW05trimR_R1.fq /nephele_data/inputs/4061-JW05trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW05trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW05trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimR_2U.fastq.gz Input Read Pairs: 105766 Both Surviving: 105764 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:16,705 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW06trimR_R1.fq /nephele_data/inputs/4061-JW06trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW06trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:22,458 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW06trimR_R1.fq /nephele_data/inputs/4061-JW06trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW06trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW06trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimR_2U.fastq.gz Input Read Pairs: 142806 Both Surviving: 142802 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:22,458 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW07trimR_R1.fq /nephele_data/inputs/4061-JW07trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW07trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:27,377 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW07trimR_R1.fq /nephele_data/inputs/4061-JW07trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW07trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW07trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimR_2U.fastq.gz Input Read Pairs: 108732 Both Surviving: 108729 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:27,377 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW08trimR_R1.fq /nephele_data/inputs/4061-JW08trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW08trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:33,142 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW08trimR_R1.fq /nephele_data/inputs/4061-JW08trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW08trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW08trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimR_2U.fastq.gz Input Read Pairs: 139727 Both Surviving: 139721 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:33,142 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW09trimR_R1.fq /nephele_data/inputs/4061-JW09trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW09trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:35,505 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW09trimR_R1.fq /nephele_data/inputs/4061-JW09trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW09trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW09trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimR_2U.fastq.gz Input Read Pairs: 46839 Both Surviving: 46835 (99.99%) Forward Only Surviving: 4 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:35,505 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW10trimR_R1.fq /nephele_data/inputs/4061-JW10trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW10trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:39,674 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW10trimR_R1.fq /nephele_data/inputs/4061-JW10trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW10trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW10trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimR_2U.fastq.gz Input Read Pairs: 83638 Both Surviving: 83630 (99.99%) Forward Only Surviving: 8 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:39,674 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW11trimR_R1.fq /nephele_data/inputs/4061-JW11trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW11trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:46,020 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW11trimR_R1.fq /nephele_data/inputs/4061-JW11trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW11trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW11trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimR_2U.fastq.gz Input Read Pairs: 143459 Both Surviving: 143456 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:46,020 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW12trimR_R1.fq /nephele_data/inputs/4061-JW12trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW12trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:50,628 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW12trimR_R1.fq /nephele_data/inputs/4061-JW12trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW12trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW12trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimR_2U.fastq.gz Input Read Pairs: 101369 Both Surviving: 101364 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:50,628 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW13trimR_R1.fq /nephele_data/inputs/4061-JW13trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW13trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:55,384 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW13trimR_R1.fq /nephele_data/inputs/4061-JW13trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW13trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW13trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimR_2U.fastq.gz Input Read Pairs: 99398 Both Surviving: 99394 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:55,384 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW14trimR_R1.fq /nephele_data/inputs/4061-JW14trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW14trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:04:59,840 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW14trimR_R1.fq /nephele_data/inputs/4061-JW14trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW14trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW14trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimR_2U.fastq.gz Input Read Pairs: 99927 Both Surviving: 99924 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:04:59,840 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW15trimR_R1.fq /nephele_data/inputs/4061-JW15trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW15trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:05,477 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW15trimR_R1.fq /nephele_data/inputs/4061-JW15trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW15trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW15trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimR_2U.fastq.gz Input Read Pairs: 126555 Both Surviving: 126551 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:05,477 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW16trimR_R1.fq /nephele_data/inputs/4061-JW16trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW16trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:11,422 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW16trimR_R1.fq /nephele_data/inputs/4061-JW16trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW16trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW16trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimR_2U.fastq.gz Input Read Pairs: 136219 Both Surviving: 136217 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:11,422 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW17trimR_R1.fq /nephele_data/inputs/4061-JW17trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW17trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:17,501 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW17trimR_R1.fq /nephele_data/inputs/4061-JW17trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW17trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW17trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimR_2U.fastq.gz Input Read Pairs: 147553 Both Surviving: 147549 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:17,501 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW18trimR_R1.fq /nephele_data/inputs/4061-JW18trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW18trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:23,530 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW18trimR_R1.fq /nephele_data/inputs/4061-JW18trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW18trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW18trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimR_2U.fastq.gz Input Read Pairs: 141647 Both Surviving: 141642 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:23,530 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW19trimR_R1.fq /nephele_data/inputs/4061-JW19trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW19trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:30,144 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW19trimR_R1.fq /nephele_data/inputs/4061-JW19trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW19trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW19trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimR_2U.fastq.gz Input Read Pairs: 153392 Both Surviving: 153385 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:30,144 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW20trimR_R1.fq /nephele_data/inputs/4061-JW20trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW20trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:35,242 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW20trimR_R1.fq /nephele_data/inputs/4061-JW20trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW20trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW20trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimR_2U.fastq.gz Input Read Pairs: 109594 Both Surviving: 109592 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:35,242 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW21trimR_R1.fq /nephele_data/inputs/4061-JW21trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW21trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:41,429 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW21trimR_R1.fq /nephele_data/inputs/4061-JW21trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW21trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW21trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimR_2U.fastq.gz Input Read Pairs: 139114 Both Surviving: 139105 (99.99%) Forward Only Surviving: 9 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:41,430 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW22trimR_R1.fq /nephele_data/inputs/4061-JW22trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW22trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:47,280 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW22trimR_R1.fq /nephele_data/inputs/4061-JW22trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW22trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW22trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimR_2U.fastq.gz Input Read Pairs: 136315 Both Surviving: 136313 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:47,280 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW23trimR_R1.fq /nephele_data/inputs/4061-JW23trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW23trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:52,959 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW23trimR_R1.fq /nephele_data/inputs/4061-JW23trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW23trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW23trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimR_2U.fastq.gz Input Read Pairs: 131570 Both Surviving: 131565 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:52,959 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW24trimR_R1.fq /nephele_data/inputs/4061-JW24trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW24trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:05:57,160 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW24trimR_R1.fq /nephele_data/inputs/4061-JW24trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW24trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW24trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimR_2U.fastq.gz Input Read Pairs: 98444 Both Surviving: 98442 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:05:57,160 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW25trimR_R1.fq /nephele_data/inputs/4061-JW25trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW25trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:03,161 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW25trimR_R1.fq /nephele_data/inputs/4061-JW25trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW25trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW25trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimR_2U.fastq.gz Input Read Pairs: 128436 Both Surviving: 128430 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:03,161 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW26trimR_R1.fq /nephele_data/inputs/4061-JW26trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW26trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:07,336 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW26trimR_R1.fq /nephele_data/inputs/4061-JW26trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW26trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW26trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimR_2U.fastq.gz Input Read Pairs: 91692 Both Surviving: 91690 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:07,336 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW27trimR_R1.fq /nephele_data/inputs/4061-JW27trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW27trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:13,807 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW27trimR_R1.fq /nephele_data/inputs/4061-JW27trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW27trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW27trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimR_2U.fastq.gz Input Read Pairs: 143557 Both Surviving: 143552 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:13,807 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW28trimR_R1.fq /nephele_data/inputs/4061-JW28trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW28trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:19,880 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW28trimR_R1.fq /nephele_data/inputs/4061-JW28trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW28trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW28trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimR_2U.fastq.gz Input Read Pairs: 139902 Both Surviving: 139896 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:19,880 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW29trimR_R1.fq /nephele_data/inputs/4061-JW29trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW29trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:25,613 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW29trimR_R1.fq /nephele_data/inputs/4061-JW29trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW29trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW29trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimR_2U.fastq.gz Input Read Pairs: 136337 Both Surviving: 136332 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:25,613 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW30trimR_R1.fq /nephele_data/inputs/4061-JW30trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW30trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:32,442 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW30trimR_R1.fq /nephele_data/inputs/4061-JW30trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW30trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW30trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimR_2U.fastq.gz Input Read Pairs: 160554 Both Surviving: 160550 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:32,442 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW31trimR_R1.fq /nephele_data/inputs/4061-JW31trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW31trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:37,522 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW31trimR_R1.fq /nephele_data/inputs/4061-JW31trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW31trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW31trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimR_2U.fastq.gz Input Read Pairs: 113826 Both Surviving: 113820 (99.99%) Forward Only Surviving: 6 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:37,522 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW32trimR_R1.fq /nephele_data/inputs/4061-JW32trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW32trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:43,659 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW32trimR_R1.fq /nephele_data/inputs/4061-JW32trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW32trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW32trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimR_2U.fastq.gz Input Read Pairs: 142001 Both Surviving: 141996 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:43,659 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW33trimR_R1.fq /nephele_data/inputs/4061-JW33trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW33trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:49,959 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW33trimR_R1.fq /nephele_data/inputs/4061-JW33trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW33trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW33trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimR_2U.fastq.gz Input Read Pairs: 144421 Both Surviving: 144414 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:49,959 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW34trimR_R1.fq /nephele_data/inputs/4061-JW34trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW34trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:06:56,920 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW34trimR_R1.fq /nephele_data/inputs/4061-JW34trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW34trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW34trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimR_2U.fastq.gz Input Read Pairs: 159990 Both Surviving: 159980 (99.99%) Forward Only Surviving: 10 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:06:56,920 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW35trimR_R1.fq /nephele_data/inputs/4061-JW35trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW35trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:03,014 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW35trimR_R1.fq /nephele_data/inputs/4061-JW35trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW35trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW35trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimR_2U.fastq.gz Input Read Pairs: 131989 Both Surviving: 131985 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:03,014 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW36trimR_R1.fq /nephele_data/inputs/4061-JW36trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW36trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:08,561 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW36trimR_R1.fq /nephele_data/inputs/4061-JW36trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW36trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW36trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimR_2U.fastq.gz Input Read Pairs: 123196 Both Surviving: 123192 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:08,561 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW37trimR_R1.fq /nephele_data/inputs/4061-JW37trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW37trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:08,757 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW37trimR_R1.fq /nephele_data/inputs/4061-JW37trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW37trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW37trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimR_2U.fastq.gz Input Read Pairs: 96 Both Surviving: 96 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:08,757 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW38trimR_R1.fq /nephele_data/inputs/4061-JW38trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW38trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-30 17:07:08,958 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW38trimR_R1.fq /nephele_data/inputs/4061-JW38trimR_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW38trimR.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW38trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimR_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimR_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimR_2U.fastq.gz Input Read Pairs: 105 Both Surviving: 105 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-30 17:07:08,958 - INFO] Quality trimming complete, see /nephele_data/outputs/multiqc_input/trimmo.log. [2022-11-30 17:07:08,958 - INFO] Run paired end merging selected. [2022-11-30 17:07:08,968 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW01trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW01trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimR_2P.fastq.gz [2022-11-30 17:07:15,246 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW01trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW01trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW01trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW01trimR_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 90420 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 90420 [FLASH] Combined pairs: 86066 [FLASH] Innie pairs: 85913 (99.82% of combined) [FLASH] Outie pairs: 153 (0.18% of combined) [FLASH] Uncombined pairs: 4354 [FLASH] Percent combined: 95.18% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.266 seconds elapsed [2022-11-30 17:07:15,246 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW02trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW02trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimR_2P.fastq.gz [2022-11-30 17:07:22,726 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW02trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW02trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW02trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW02trimR_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 110173 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 110173 [FLASH] Combined pairs: 106174 [FLASH] Innie pairs: 105809 (99.66% of combined) [FLASH] Outie pairs: 365 (0.34% of combined) [FLASH] Uncombined pairs: 3999 [FLASH] Percent combined: 96.37% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.469 seconds elapsed [2022-11-30 17:07:22,726 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW03trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW03trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimR_2P.fastq.gz [2022-11-30 17:07:31,920 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW03trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW03trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW03trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW03trimR_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 146429 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 146429 [FLASH] Combined pairs: 142302 [FLASH] Innie pairs: 141411 (99.37% of combined) [FLASH] Outie pairs: 891 (0.63% of combined) [FLASH] Uncombined pairs: 4127 [FLASH] Percent combined: 97.18% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.183 seconds elapsed [2022-11-30 17:07:31,920 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW04trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW04trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimR_2P.fastq.gz [2022-11-30 17:07:39,908 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW04trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW04trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW04trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW04trimR_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 117858 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 117858 [FLASH] Combined pairs: 114206 [FLASH] Innie pairs: 113710 (99.57% of combined) [FLASH] Outie pairs: 496 (0.43% of combined) [FLASH] Uncombined pairs: 3652 [FLASH] Percent combined: 96.90% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.978 seconds elapsed [2022-11-30 17:07:39,909 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW05trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW05trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimR_2P.fastq.gz [2022-11-30 17:07:46,940 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW05trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW05trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW05trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW05trimR_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 105764 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 105764 [FLASH] Combined pairs: 100063 [FLASH] Innie pairs: 99764 (99.70% of combined) [FLASH] Outie pairs: 299 (0.30% of combined) [FLASH] Uncombined pairs: 5701 [FLASH] Percent combined: 94.61% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.021 seconds elapsed [2022-11-30 17:07:46,940 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW06trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW06trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimR_2P.fastq.gz [2022-11-30 17:07:55,621 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW06trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW06trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW06trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW06trimR_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 142802 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 142802 [FLASH] Combined pairs: 139544 [FLASH] Innie pairs: 139273 (99.81% of combined) [FLASH] Outie pairs: 271 (0.19% of combined) [FLASH] Uncombined pairs: 3258 [FLASH] Percent combined: 97.72% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.670 seconds elapsed [2022-11-30 17:07:55,621 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW07trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW07trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimR_2P.fastq.gz [2022-11-30 17:08:03,005 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW07trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW07trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW07trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW07trimR_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 108729 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 108729 [FLASH] Combined pairs: 104613 [FLASH] Innie pairs: 104522 (99.91% of combined) [FLASH] Outie pairs: 91 (0.09% of combined) [FLASH] Uncombined pairs: 4116 [FLASH] Percent combined: 96.21% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.373 seconds elapsed [2022-11-30 17:08:03,005 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW08trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW08trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimR_2P.fastq.gz [2022-11-30 17:08:11,610 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW08trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW08trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW08trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW08trimR_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 139721 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 139721 [FLASH] Combined pairs: 135206 [FLASH] Innie pairs: 134882 (99.76% of combined) [FLASH] Outie pairs: 324 (0.24% of combined) [FLASH] Uncombined pairs: 4515 [FLASH] Percent combined: 96.77% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.594 seconds elapsed [2022-11-30 17:08:11,610 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW09trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW09trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimR_2P.fastq.gz [2022-11-30 17:08:14,874 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW09trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW09trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW09trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW09trimR_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 46835 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 46835 [FLASH] Combined pairs: 43747 [FLASH] Innie pairs: 43640 (99.76% of combined) [FLASH] Outie pairs: 107 (0.24% of combined) [FLASH] Uncombined pairs: 3088 [FLASH] Percent combined: 93.41% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.253 seconds elapsed [2022-11-30 17:08:14,874 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW10trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW10trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimR_2P.fastq.gz [2022-11-30 17:08:20,683 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW10trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW10trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW10trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW10trimR_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 83630 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 83630 [FLASH] Combined pairs: 75658 [FLASH] Innie pairs: 75220 (99.42% of combined) [FLASH] Outie pairs: 438 (0.58% of combined) [FLASH] Uncombined pairs: 7972 [FLASH] Percent combined: 90.47% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.799 seconds elapsed [2022-11-30 17:08:20,683 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW11trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW11trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimR_2P.fastq.gz [2022-11-30 17:08:30,299 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW11trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW11trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW11trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW11trimR_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 143456 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 143456 [FLASH] Combined pairs: 138250 [FLASH] Innie pairs: 137556 (99.50% of combined) [FLASH] Outie pairs: 694 (0.50% of combined) [FLASH] Uncombined pairs: 5206 [FLASH] Percent combined: 96.37% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.605 seconds elapsed [2022-11-30 17:08:30,299 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW12trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW12trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimR_2P.fastq.gz [2022-11-30 17:08:37,012 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW12trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW12trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW12trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW12trimR_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 101364 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 101364 [FLASH] Combined pairs: 97661 [FLASH] Innie pairs: 97307 (99.64% of combined) [FLASH] Outie pairs: 354 (0.36% of combined) [FLASH] Uncombined pairs: 3703 [FLASH] Percent combined: 96.35% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.703 seconds elapsed [2022-11-30 17:08:37,012 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW13trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW13trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimR_2P.fastq.gz [2022-11-30 17:08:44,184 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW13trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW13trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW13trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW13trimR_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 99394 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 99394 [FLASH] Combined pairs: 93918 [FLASH] Innie pairs: 93832 (99.91% of combined) [FLASH] Outie pairs: 86 (0.09% of combined) [FLASH] Uncombined pairs: 5476 [FLASH] Percent combined: 94.49% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.162 seconds elapsed [2022-11-30 17:08:44,185 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW14trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW14trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimR_2P.fastq.gz [2022-11-30 17:08:50,948 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW14trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW14trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW14trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW14trimR_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 99924 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 99924 [FLASH] Combined pairs: 96131 [FLASH] Innie pairs: 95978 (99.84% of combined) [FLASH] Outie pairs: 153 (0.16% of combined) [FLASH] Uncombined pairs: 3793 [FLASH] Percent combined: 96.20% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.753 seconds elapsed [2022-11-30 17:08:50,949 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW15trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW15trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimR_2P.fastq.gz [2022-11-30 17:08:59,258 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW15trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW15trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW15trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW15trimR_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 126551 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 126551 [FLASH] Combined pairs: 122316 [FLASH] Innie pairs: 121364 (99.22% of combined) [FLASH] Outie pairs: 952 (0.78% of combined) [FLASH] Uncombined pairs: 4235 [FLASH] Percent combined: 96.65% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.299 seconds elapsed [2022-11-30 17:08:59,258 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW16trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW16trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimR_2P.fastq.gz [2022-11-30 17:09:08,294 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW16trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW16trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW16trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW16trimR_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 136217 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 136217 [FLASH] Combined pairs: 131966 [FLASH] Innie pairs: 130583 (98.95% of combined) [FLASH] Outie pairs: 1383 (1.05% of combined) [FLASH] Uncombined pairs: 4251 [FLASH] Percent combined: 96.88% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.025 seconds elapsed [2022-11-30 17:09:08,294 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW17trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW17trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimR_2P.fastq.gz [2022-11-30 17:09:17,672 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW17trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW17trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW17trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW17trimR_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 147549 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 147549 [FLASH] Combined pairs: 143987 [FLASH] Innie pairs: 143434 (99.62% of combined) [FLASH] Outie pairs: 553 (0.38% of combined) [FLASH] Uncombined pairs: 3562 [FLASH] Percent combined: 97.59% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.367 seconds elapsed [2022-11-30 17:09:17,672 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW18trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW18trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimR_2P.fastq.gz [2022-11-30 17:09:26,845 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW18trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW18trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW18trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW18trimR_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 141642 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 141642 [FLASH] Combined pairs: 138108 [FLASH] Innie pairs: 137691 (99.70% of combined) [FLASH] Outie pairs: 417 (0.30% of combined) [FLASH] Uncombined pairs: 3534 [FLASH] Percent combined: 97.50% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.162 seconds elapsed [2022-11-30 17:09:26,845 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW19trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW19trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimR_2P.fastq.gz [2022-11-30 17:09:37,085 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW19trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW19trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW19trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW19trimR_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 153385 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 153385 [FLASH] Combined pairs: 148127 [FLASH] Innie pairs: 147922 (99.86% of combined) [FLASH] Outie pairs: 205 (0.14% of combined) [FLASH] Uncombined pairs: 5258 [FLASH] Percent combined: 96.57% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 10.229 seconds elapsed [2022-11-30 17:09:37,085 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW20trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW20trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimR_2P.fastq.gz [2022-11-30 17:09:44,652 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW20trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW20trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW20trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW20trimR_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 109592 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 109592 [FLASH] Combined pairs: 105716 [FLASH] Innie pairs: 105312 (99.62% of combined) [FLASH] Outie pairs: 404 (0.38% of combined) [FLASH] Uncombined pairs: 3876 [FLASH] Percent combined: 96.46% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.555 seconds elapsed [2022-11-30 17:09:44,652 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW21trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW21trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimR_2P.fastq.gz [2022-11-30 17:09:53,497 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW21trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW21trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW21trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW21trimR_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 139105 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 139105 [FLASH] Combined pairs: 133153 [FLASH] Innie pairs: 132335 (99.39% of combined) [FLASH] Outie pairs: 818 (0.61% of combined) [FLASH] Uncombined pairs: 5952 [FLASH] Percent combined: 95.72% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.834 seconds elapsed [2022-11-30 17:09:53,497 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW22trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW22trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimR_2P.fastq.gz [2022-11-30 17:10:02,538 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW22trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW22trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW22trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW22trimR_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 136313 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 136313 [FLASH] Combined pairs: 132186 [FLASH] Innie pairs: 131200 (99.25% of combined) [FLASH] Outie pairs: 986 (0.75% of combined) [FLASH] Uncombined pairs: 4127 [FLASH] Percent combined: 96.97% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.030 seconds elapsed [2022-11-30 17:10:02,539 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW23trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW23trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimR_2P.fastq.gz [2022-11-30 17:10:11,273 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW23trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW23trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW23trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW23trimR_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 131565 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 131565 [FLASH] Combined pairs: 127330 [FLASH] Innie pairs: 126698 (99.50% of combined) [FLASH] Outie pairs: 632 (0.50% of combined) [FLASH] Uncombined pairs: 4235 [FLASH] Percent combined: 96.78% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.724 seconds elapsed [2022-11-30 17:10:11,274 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW24trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW24trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimR_2P.fastq.gz [2022-11-30 17:10:17,763 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW24trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW24trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW24trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW24trimR_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 98442 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 98442 [FLASH] Combined pairs: 94172 [FLASH] Innie pairs: 93817 (99.62% of combined) [FLASH] Outie pairs: 355 (0.38% of combined) [FLASH] Uncombined pairs: 4270 [FLASH] Percent combined: 95.66% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.479 seconds elapsed [2022-11-30 17:10:17,764 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW25trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW25trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimR_2P.fastq.gz [2022-11-30 17:10:26,933 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW25trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW25trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW25trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW25trimR_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 128430 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 128430 [FLASH] Combined pairs: 124244 [FLASH] Innie pairs: 124048 (99.84% of combined) [FLASH] Outie pairs: 196 (0.16% of combined) [FLASH] Uncombined pairs: 4186 [FLASH] Percent combined: 96.74% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.159 seconds elapsed [2022-11-30 17:10:26,933 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW26trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW26trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimR_2P.fastq.gz [2022-11-30 17:10:33,147 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW26trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW26trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW26trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW26trimR_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 91690 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 91690 [FLASH] Combined pairs: 86868 [FLASH] Innie pairs: 86531 (99.61% of combined) [FLASH] Outie pairs: 337 (0.39% of combined) [FLASH] Uncombined pairs: 4822 [FLASH] Percent combined: 94.74% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.203 seconds elapsed [2022-11-30 17:10:33,147 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW27trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW27trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimR_2P.fastq.gz [2022-11-30 17:10:42,845 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW27trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW27trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW27trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW27trimR_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 143552 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 143552 [FLASH] Combined pairs: 138025 [FLASH] Innie pairs: 137246 (99.44% of combined) [FLASH] Outie pairs: 779 (0.56% of combined) [FLASH] Uncombined pairs: 5527 [FLASH] Percent combined: 96.15% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.687 seconds elapsed [2022-11-30 17:10:42,846 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW28trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW28trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimR_2P.fastq.gz [2022-11-30 17:10:52,245 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW28trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW28trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW28trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW28trimR_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 139896 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 139896 [FLASH] Combined pairs: 135344 [FLASH] Innie pairs: 134568 (99.43% of combined) [FLASH] Outie pairs: 776 (0.57% of combined) [FLASH] Uncombined pairs: 4552 [FLASH] Percent combined: 96.75% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.389 seconds elapsed [2022-11-30 17:10:52,245 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW29trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW29trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimR_2P.fastq.gz [2022-11-30 17:11:00,880 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW29trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW29trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW29trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW29trimR_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 136332 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 136332 [FLASH] Combined pairs: 132711 [FLASH] Innie pairs: 132342 (99.72% of combined) [FLASH] Outie pairs: 369 (0.28% of combined) [FLASH] Uncombined pairs: 3621 [FLASH] Percent combined: 97.34% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.624 seconds elapsed [2022-11-30 17:11:00,880 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW30trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW30trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimR_2P.fastq.gz [2022-11-30 17:11:11,578 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW30trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW30trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW30trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW30trimR_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 160550 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 160550 [FLASH] Combined pairs: 155471 [FLASH] Innie pairs: 154864 (99.61% of combined) [FLASH] Outie pairs: 607 (0.39% of combined) [FLASH] Uncombined pairs: 5079 [FLASH] Percent combined: 96.84% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 10.687 seconds elapsed [2022-11-30 17:11:11,578 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW31trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW31trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimR_2P.fastq.gz [2022-11-30 17:11:19,358 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW31trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW31trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW31trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW31trimR_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 113820 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 113820 [FLASH] Combined pairs: 109432 [FLASH] Innie pairs: 109280 (99.86% of combined) [FLASH] Outie pairs: 152 (0.14% of combined) [FLASH] Uncombined pairs: 4388 [FLASH] Percent combined: 96.14% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.769 seconds elapsed [2022-11-30 17:11:19,359 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW32trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW32trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimR_2P.fastq.gz [2022-11-30 17:11:28,607 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW32trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW32trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW32trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW32trimR_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 141996 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 141996 [FLASH] Combined pairs: 137639 [FLASH] Innie pairs: 136821 (99.41% of combined) [FLASH] Outie pairs: 818 (0.59% of combined) [FLASH] Uncombined pairs: 4357 [FLASH] Percent combined: 96.93% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.237 seconds elapsed [2022-11-30 17:11:28,607 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW33trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW33trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimR_2P.fastq.gz [2022-11-30 17:11:38,442 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW33trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW33trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW33trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW33trimR_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 144414 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 144414 [FLASH] Combined pairs: 140289 [FLASH] Innie pairs: 139578 (99.49% of combined) [FLASH] Outie pairs: 711 (0.51% of combined) [FLASH] Uncombined pairs: 4125 [FLASH] Percent combined: 97.14% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.823 seconds elapsed [2022-11-30 17:11:38,442 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW34trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW34trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimR_2P.fastq.gz [2022-11-30 17:11:48,883 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW34trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW34trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW34trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW34trimR_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 159980 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 159980 [FLASH] Combined pairs: 154734 [FLASH] Innie pairs: 153924 (99.48% of combined) [FLASH] Outie pairs: 810 (0.52% of combined) [FLASH] Uncombined pairs: 5246 [FLASH] Percent combined: 96.72% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 10.430 seconds elapsed [2022-11-30 17:11:48,883 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW35trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW35trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimR_2P.fastq.gz [2022-11-30 17:11:57,989 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW35trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW35trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW35trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW35trimR_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 131985 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 131985 [FLASH] Combined pairs: 127554 [FLASH] Innie pairs: 126744 (99.36% of combined) [FLASH] Outie pairs: 810 (0.64% of combined) [FLASH] Uncombined pairs: 4431 [FLASH] Percent combined: 96.64% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 9.094 seconds elapsed [2022-11-30 17:11:57,989 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW36trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW36trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimR_2P.fastq.gz [2022-11-30 17:12:06,642 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW36trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW36trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW36trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW36trimR_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 123192 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 123192 [FLASH] Combined pairs: 117229 [FLASH] Innie pairs: 116558 (99.43% of combined) [FLASH] Outie pairs: 671 (0.57% of combined) [FLASH] Uncombined pairs: 5963 [FLASH] Percent combined: 95.16% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.642 seconds elapsed [2022-11-30 17:12:06,642 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW37trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW37trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimR_2P.fastq.gz [2022-11-30 17:12:06,664 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW37trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW37trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW37trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW37trimR_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 96 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 96 [FLASH] Combined pairs: 15 [FLASH] Innie pairs: 13 (86.67% of combined) [FLASH] Outie pairs: 2 (13.33% of combined) [FLASH] Uncombined pairs: 81 [FLASH] Percent combined: 15.62% [FLASH] [FLASH] Writing histogram files. [FLASH] WARNING: An unexpectedly high proportion of combined pairs (13.33%) 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] 0.013 seconds elapsed [FLASH] Finished with 1 warning (see above) [2022-11-30 17:12:06,665 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW38trimR_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW38trimR_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimR_2P.fastq.gz [2022-11-30 17:12:06,687 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW38trimR_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW38trimR_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW38trimR_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimR_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimR_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimR_merged.hist [FLASH] /nephele_data/outputs/merged//JW38trimR_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 105 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 105 [FLASH] Combined pairs: 10 [FLASH] Innie pairs: 8 (80.00% of combined) [FLASH] Outie pairs: 2 (20.00% of combined) [FLASH] Uncombined pairs: 95 [FLASH] Percent combined: 9.52% [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] 0.014 seconds elapsed [FLASH] Finished with 1 warning (see above) [2022-11-30 17:12:06,687 - INFO] Finished paired end merging. [2022-11-30 17:12:06,687 - INFO] Trying to link hist files for multiqc analysis. [2022-11-30 17:12:06,688 - INFO] Finished linking. [2022-11-30 17:12:06,689 - INFO] Trying to run multiqc on /nephele_data/outputs/multiqc_input/. [2022-11-30 17:12:06,689 - INFO] Linking logfile to multiqc inputs directory, /nephele_data/outputs/multiqc_input/. [2022-11-30 17:12:06,689 - INFO] Finished linking. [2022-11-30 17:12:19,786 - INFO] /// MultiQC 🔍 | v1.13.dev0 | multiqc | Report title: Ill-v34-R_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/Ill-v34-R_221130_multiqc_report.html | multiqc | Data : nephele_data/outputs/Ill-v34-R_221130_multiqc_report_data | multiqc | MultiQC complete [2022-11-30 17:12:19,786 - INFO] Finished multiqc. [2022-11-30 17:12:19,786 - INFO] QC pipeline complete. [2022-11-30 17:12:19,786 - INFO] 0