[2022-11-28 20:33:47,320 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.21.5, tag: Nephele_2022_October_06, commit: c1eb66c [2022-11-28 20:33:47,320 - INFO] Python version: 3.8.13 [2022-11-28 20:33:47,321 - INFO] Current time: 2022-11-28 20:33 [2022-11-28 20:33:47,321 - INFO] Pipeline name: QC Reads [2022-11-28 20:33:47,565 - INFO] Job Description: EM-v4 [2022-11-28 20:33:47,565 - INFO] Job parameters job_id: 582417d93f82 inputs_dir: None outputs_dir: None map_file: <_io.TextIOWrapper name='/nephele_data/inputs/EM-v4-Y_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 [2022-11-28 20:33:47,565 - INFO] Checking Mapfile for Gzipped inputs. [2022-11-28 20:33:47,565 - INFO] Gzipped files listed in map file, attempting to rm .gz extension. [2022-11-28 20:33:47,566 - INFO] Done. Attempting file decompression. [2022-11-28 20:34:20,651 - INFO] Finished decompression. [2022-11-28 20:34:20,651 - INFO] Starting pipe... [2022-11-28 20:34:20,659 - INFO] Trying to generate samples [2022-11-28 20:34:20,660 - INFO] Starting Fastqc, outputs in /nephele_data/outputs/multiqc_input/. [2022-11-28 20:34:20,660 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW01trimY_R1.fq [2022-11-28 20:34:24,177 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW01trimY_R2.fq [2022-11-28 20:34:27,405 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW02trimY_R1.fq [2022-11-28 20:34:30,671 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW02trimY_R2.fq [2022-11-28 20:34:33,915 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW03trimY_R1.fq [2022-11-28 20:34:37,139 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW03trimY_R2.fq [2022-11-28 20:34:40,364 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW04trimY_R1.fq [2022-11-28 20:34:43,607 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW04trimY_R2.fq [2022-11-28 20:34:45,836 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW05trimY_R1.fq [2022-11-28 20:34:49,062 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW05trimY_R2.fq [2022-11-28 20:34:52,297 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW06trimY_R1.fq [2022-11-28 20:34:55,522 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW06trimY_R2.fq [2022-11-28 20:34:58,747 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW07trimY_R1.fq [2022-11-28 20:35:02,002 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW07trimY_R2.fq [2022-11-28 20:35:06,242 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW08trimY_R1.fq [2022-11-28 20:35:09,476 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW08trimY_R2.fq [2022-11-28 20:35:12,702 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW09trimY_R1.fq [2022-11-28 20:35:15,927 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW09trimY_R2.fq [2022-11-28 20:35:19,152 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW10trimY_R1.fq [2022-11-28 20:35:22,380 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW10trimY_R2.fq [2022-11-28 20:35:25,605 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW11trimY_R1.fq [2022-11-28 20:35:28,831 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW11trimY_R2.fq [2022-11-28 20:35:32,056 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW12trimY_R1.fq [2022-11-28 20:35:36,284 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW12trimY_R2.fq [2022-11-28 20:35:39,587 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW13trimY_R1.fq [2022-11-28 20:35:43,814 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW13trimY_R2.fq [2022-11-28 20:35:48,049 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW14trimY_R1.fq [2022-11-28 20:35:51,271 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW14trimY_R2.fq [2022-11-28 20:35:54,526 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW15trimY_R1.fq [2022-11-28 20:35:57,752 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW15trimY_R2.fq [2022-11-28 20:36:00,996 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW16trimY_R1.fq [2022-11-28 20:36:04,221 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW16trimY_R2.fq [2022-11-28 20:36:07,457 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW17trimY_R1.fq [2022-11-28 20:36:10,682 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW17trimY_R2.fq [2022-11-28 20:36:13,907 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW18trimY_R1.fq [2022-11-28 20:36:18,152 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW18trimY_R2.fq [2022-11-28 20:36:22,382 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW19trimY_R1.fq [2022-11-28 20:36:26,608 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW19trimY_R2.fq [2022-11-28 20:36:29,874 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW20trimY_R1.fq [2022-11-28 20:36:33,096 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW20trimY_R2.fq [2022-11-28 20:36:36,320 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW21trimY_R1.fq [2022-11-28 20:36:39,544 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW21trimY_R2.fq [2022-11-28 20:36:42,772 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW22trimY_R1.fq [2022-11-28 20:36:45,997 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW22trimY_R2.fq [2022-11-28 20:36:49,224 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW23trimY_R1.fq [2022-11-28 20:36:52,449 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW23trimY_R2.fq [2022-11-28 20:36:55,676 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW24trimY_R1.fq [2022-11-28 20:36:58,902 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW24trimY_R2.fq [2022-11-28 20:37:02,128 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW25trimY_R1.fq [2022-11-28 20:37:05,352 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW25trimY_R2.fq [2022-11-28 20:37:08,576 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW26trimY_R1.fq [2022-11-28 20:37:11,805 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW26trimY_R2.fq [2022-11-28 20:37:15,030 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW27trimY_R1.fq [2022-11-28 20:37:18,255 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW27trimY_R2.fq [2022-11-28 20:37:21,479 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW28trimY_R1.fq [2022-11-28 20:37:24,704 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW28trimY_R2.fq [2022-11-28 20:37:27,928 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW29trimY_R1.fq [2022-11-28 20:37:31,153 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW29trimY_R2.fq [2022-11-28 20:37:34,379 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW30trimY_R1.fq [2022-11-28 20:37:37,674 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW30trimY_R2.fq [2022-11-28 20:37:40,898 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW31trimY_R1.fq [2022-11-28 20:37:44,123 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW31trimY_R2.fq [2022-11-28 20:37:47,348 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW32trimY_R1.fq [2022-11-28 20:37:50,613 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW32trimY_R2.fq [2022-11-28 20:37:53,869 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW33trimY_R1.fq [2022-11-28 20:37:57,095 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW33trimY_R2.fq [2022-11-28 20:38:00,350 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW34trimY_R1.fq [2022-11-28 20:38:03,583 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW34trimY_R2.fq [2022-11-28 20:38:06,808 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW35trimY_R1.fq [2022-11-28 20:38:10,033 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW35trimY_R2.fq [2022-11-28 20:38:13,266 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW36trimY_R1.fq [2022-11-28 20:38:16,501 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW36trimY_R2.fq [2022-11-28 20:38:19,723 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW37trimY_R1.fq [2022-11-28 20:38:22,027 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW37trimY_R2.fq [2022-11-28 20:38:24,252 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW38trimY_R1.fq [2022-11-28 20:38:26,475 - INFO] trying to run: fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/4061-JW38trimY_R2.fq [2022-11-28 20:38:28,698 - INFO] Finished Fastqc, see /nephele_data/outputs/multiqc_input/ for outputs. [2022-11-28 20:38:28,699 - INFO] Run Trimmomatic quality trimming selected. [2022-11-28 20:38:28,699 - INFO] Trying to create /nephele_data/outputs/qtrimmed_seqs/. [2022-11-28 20:38:28,708 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW01trimY_R1.fq /nephele_data/inputs/4061-JW01trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW01trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:31,897 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW01trimY_R1.fq /nephele_data/inputs/4061-JW01trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW01trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW01trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimY_2U.fastq.gz Input Read Pairs: 63989 Both Surviving: 63986 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:31,897 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW02trimY_R1.fq /nephele_data/inputs/4061-JW02trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW02trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:36,671 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW02trimY_R1.fq /nephele_data/inputs/4061-JW02trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW02trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW02trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimY_2U.fastq.gz Input Read Pairs: 123846 Both Surviving: 123842 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:36,671 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW03trimY_R1.fq /nephele_data/inputs/4061-JW03trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW03trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:39,143 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW03trimY_R1.fq /nephele_data/inputs/4061-JW03trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW03trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW03trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimY_2U.fastq.gz Input Read Pairs: 51505 Both Surviving: 51504 (100.00%) Forward Only Surviving: 1 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:39,143 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW04trimY_R1.fq /nephele_data/inputs/4061-JW04trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW04trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:41,001 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW04trimY_R1.fq /nephele_data/inputs/4061-JW04trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW04trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW04trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimY_2U.fastq.gz Input Read Pairs: 29416 Both Surviving: 29415 (100.00%) Forward Only Surviving: 1 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:41,002 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW05trimY_R1.fq /nephele_data/inputs/4061-JW05trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW05trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:45,947 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW05trimY_R1.fq /nephele_data/inputs/4061-JW05trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW05trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW05trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimY_2U.fastq.gz Input Read Pairs: 118528 Both Surviving: 118524 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:45,947 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW06trimY_R1.fq /nephele_data/inputs/4061-JW06trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW06trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:49,784 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW06trimY_R1.fq /nephele_data/inputs/4061-JW06trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW06trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW06trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimY_2U.fastq.gz Input Read Pairs: 98479 Both Surviving: 98476 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:49,784 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW07trimY_R1.fq /nephele_data/inputs/4061-JW07trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW07trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:38:55,204 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW07trimY_R1.fq /nephele_data/inputs/4061-JW07trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW07trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW07trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimY_2U.fastq.gz Input Read Pairs: 126165 Both Surviving: 126165 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:38:55,204 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW08trimY_R1.fq /nephele_data/inputs/4061-JW08trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW08trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:02,644 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW08trimY_R1.fq /nephele_data/inputs/4061-JW08trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW08trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW08trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimY_2U.fastq.gz Input Read Pairs: 187475 Both Surviving: 187468 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:02,644 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW09trimY_R1.fq /nephele_data/inputs/4061-JW09trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW09trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:07,964 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW09trimY_R1.fq /nephele_data/inputs/4061-JW09trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW09trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW09trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimY_2U.fastq.gz Input Read Pairs: 129940 Both Surviving: 129933 (99.99%) Forward Only Surviving: 7 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:07,965 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW10trimY_R1.fq /nephele_data/inputs/4061-JW10trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW10trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:13,999 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW10trimY_R1.fq /nephele_data/inputs/4061-JW10trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW10trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW10trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimY_2U.fastq.gz Input Read Pairs: 142480 Both Surviving: 142474 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:13,999 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW11trimY_R1.fq /nephele_data/inputs/4061-JW11trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW11trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:19,191 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW11trimY_R1.fq /nephele_data/inputs/4061-JW11trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW11trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW11trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimY_2U.fastq.gz Input Read Pairs: 115682 Both Surviving: 115678 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:19,191 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW12trimY_R1.fq /nephele_data/inputs/4061-JW12trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW12trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:26,014 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW12trimY_R1.fq /nephele_data/inputs/4061-JW12trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW12trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW12trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimY_2U.fastq.gz Input Read Pairs: 163100 Both Surviving: 163096 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:26,014 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW13trimY_R1.fq /nephele_data/inputs/4061-JW13trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW13trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:33,834 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW13trimY_R1.fq /nephele_data/inputs/4061-JW13trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW13trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW13trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimY_2U.fastq.gz Input Read Pairs: 181926 Both Surviving: 181922 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:33,834 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW14trimY_R1.fq /nephele_data/inputs/4061-JW14trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW14trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:40,984 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW14trimY_R1.fq /nephele_data/inputs/4061-JW14trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW14trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW14trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimY_2U.fastq.gz Input Read Pairs: 169552 Both Surviving: 169548 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:40,985 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW15trimY_R1.fq /nephele_data/inputs/4061-JW15trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW15trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:46,561 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW15trimY_R1.fq /nephele_data/inputs/4061-JW15trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW15trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW15trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimY_2U.fastq.gz Input Read Pairs: 133332 Both Surviving: 133324 (99.99%) Forward Only Surviving: 8 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:46,561 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW16trimY_R1.fq /nephele_data/inputs/4061-JW16trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW16trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:52,121 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW16trimY_R1.fq /nephele_data/inputs/4061-JW16trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW16trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW16trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimY_2U.fastq.gz Input Read Pairs: 132588 Both Surviving: 132581 (99.99%) Forward Only Surviving: 7 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:52,121 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW17trimY_R1.fq /nephele_data/inputs/4061-JW17trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW17trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:39:55,436 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW17trimY_R1.fq /nephele_data/inputs/4061-JW17trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW17trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW17trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimY_2U.fastq.gz Input Read Pairs: 74627 Both Surviving: 74623 (99.99%) Forward Only Surviving: 4 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:39:55,436 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW18trimY_R1.fq /nephele_data/inputs/4061-JW18trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW18trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:04,858 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW18trimY_R1.fq /nephele_data/inputs/4061-JW18trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW18trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW18trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimY_2U.fastq.gz Input Read Pairs: 243218 Both Surviving: 243211 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:04,858 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW19trimY_R1.fq /nephele_data/inputs/4061-JW19trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW19trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:11,891 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW19trimY_R1.fq /nephele_data/inputs/4061-JW19trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW19trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW19trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimY_2U.fastq.gz Input Read Pairs: 169414 Both Surviving: 169407 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:11,891 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW20trimY_R1.fq /nephele_data/inputs/4061-JW20trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW20trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:17,176 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW20trimY_R1.fq /nephele_data/inputs/4061-JW20trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW20trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW20trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimY_2U.fastq.gz Input Read Pairs: 128357 Both Surviving: 128355 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:17,176 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW21trimY_R1.fq /nephele_data/inputs/4061-JW21trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW21trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:23,270 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW21trimY_R1.fq /nephele_data/inputs/4061-JW21trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW21trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW21trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimY_2U.fastq.gz Input Read Pairs: 149955 Both Surviving: 149953 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:23,270 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW22trimY_R1.fq /nephele_data/inputs/4061-JW22trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW22trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:27,803 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW22trimY_R1.fq /nephele_data/inputs/4061-JW22trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW22trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW22trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimY_2U.fastq.gz Input Read Pairs: 97031 Both Surviving: 97029 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:27,803 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW23trimY_R1.fq /nephele_data/inputs/4061-JW23trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW23trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:31,433 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW23trimY_R1.fq /nephele_data/inputs/4061-JW23trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW23trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW23trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimY_2U.fastq.gz Input Read Pairs: 84689 Both Surviving: 84685 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:31,434 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW24trimY_R1.fq /nephele_data/inputs/4061-JW24trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW24trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:38,171 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW24trimY_R1.fq /nephele_data/inputs/4061-JW24trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW24trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW24trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimY_2U.fastq.gz Input Read Pairs: 160717 Both Surviving: 160708 (99.99%) Forward Only Surviving: 9 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:38,171 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW25trimY_R1.fq /nephele_data/inputs/4061-JW25trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW25trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:43,181 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW25trimY_R1.fq /nephele_data/inputs/4061-JW25trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW25trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW25trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimY_2U.fastq.gz Input Read Pairs: 112320 Both Surviving: 112315 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:43,181 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW26trimY_R1.fq /nephele_data/inputs/4061-JW26trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW26trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:48,986 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW26trimY_R1.fq /nephele_data/inputs/4061-JW26trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW26trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW26trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimY_2U.fastq.gz Input Read Pairs: 144401 Both Surviving: 144399 (100.00%) Forward Only Surviving: 2 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:48,986 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW27trimY_R1.fq /nephele_data/inputs/4061-JW27trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW27trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:40:54,342 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW27trimY_R1.fq /nephele_data/inputs/4061-JW27trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW27trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW27trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimY_2U.fastq.gz Input Read Pairs: 121143 Both Surviving: 121139 (100.00%) Forward Only Surviving: 4 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:40:54,342 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW28trimY_R1.fq /nephele_data/inputs/4061-JW28trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW28trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:00,138 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW28trimY_R1.fq /nephele_data/inputs/4061-JW28trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW28trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW28trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimY_2U.fastq.gz Input Read Pairs: 130203 Both Surviving: 130197 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:00,138 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW29trimY_R1.fq /nephele_data/inputs/4061-JW29trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW29trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:05,392 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW29trimY_R1.fq /nephele_data/inputs/4061-JW29trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW29trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW29trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimY_2U.fastq.gz Input Read Pairs: 121673 Both Surviving: 121664 (99.99%) Forward Only Surviving: 9 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:05,392 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW30trimY_R1.fq /nephele_data/inputs/4061-JW30trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW30trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:11,049 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW30trimY_R1.fq /nephele_data/inputs/4061-JW30trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW30trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW30trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimY_2U.fastq.gz Input Read Pairs: 138619 Both Surviving: 138614 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:11,049 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW31trimY_R1.fq /nephele_data/inputs/4061-JW31trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW31trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:13,174 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW31trimY_R1.fq /nephele_data/inputs/4061-JW31trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW31trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW31trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimY_2U.fastq.gz Input Read Pairs: 35069 Both Surviving: 35068 (100.00%) Forward Only Surviving: 1 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:13,174 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW32trimY_R1.fq /nephele_data/inputs/4061-JW32trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW32trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:18,827 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW32trimY_R1.fq /nephele_data/inputs/4061-JW32trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW32trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW32trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimY_2U.fastq.gz Input Read Pairs: 141490 Both Surviving: 141487 (100.00%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:18,827 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW33trimY_R1.fq /nephele_data/inputs/4061-JW33trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW33trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:24,809 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW33trimY_R1.fq /nephele_data/inputs/4061-JW33trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW33trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW33trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimY_2U.fastq.gz Input Read Pairs: 148612 Both Surviving: 148606 (100.00%) Forward Only Surviving: 6 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:24,810 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW34trimY_R1.fq /nephele_data/inputs/4061-JW34trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW34trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:30,497 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW34trimY_R1.fq /nephele_data/inputs/4061-JW34trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW34trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW34trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimY_2U.fastq.gz Input Read Pairs: 136217 Both Surviving: 136212 (100.00%) Forward Only Surviving: 5 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:30,498 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW35trimY_R1.fq /nephele_data/inputs/4061-JW35trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW35trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:37,130 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW35trimY_R1.fq /nephele_data/inputs/4061-JW35trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW35trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW35trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimY_2U.fastq.gz Input Read Pairs: 163039 Both Surviving: 163029 (99.99%) Forward Only Surviving: 10 (0.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:37,131 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW36trimY_R1.fq /nephele_data/inputs/4061-JW36trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW36trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:42,265 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW36trimY_R1.fq /nephele_data/inputs/4061-JW36trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW36trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW36trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimY_2U.fastq.gz Input Read Pairs: 119093 Both Surviving: 119092 (100.00%) Forward Only Surviving: 1 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:42,265 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW37trimY_R1.fq /nephele_data/inputs/4061-JW37trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW37trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:42,530 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW37trimY_R1.fq /nephele_data/inputs/4061-JW37trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW37trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW37trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimY_2U.fastq.gz Input Read Pairs: 551 Both Surviving: 551 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:42,530 - INFO] Trying to run trimmomatic PE -phred33 /nephele_data/inputs/4061-JW38trimY_R1.fq /nephele_data/inputs/4061-JW38trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW38trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 [2022-11-28 20:41:42,777 - INFO] TrimmomaticPE: Started with arguments: -threads 16 -phred33 /nephele_data/inputs/4061-JW38trimY_R1.fq /nephele_data/inputs/4061-JW38trimY_R2.fq -baseout /nephele_data/outputs/qtrimmed_seqs/JW38trimY.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0 Using templated Output files: /nephele_data/outputs/qtrimmed_seqs/JW38trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimY_1U.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimY_2P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimY_2U.fastq.gz Input Read Pairs: 529 Both Surviving: 529 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully [2022-11-28 20:41:42,778 - INFO] Quality trimming complete, see /nephele_data/outputs/multiqc_input/trimmo.log. [2022-11-28 20:41:42,778 - INFO] Run paired end merging selected. [2022-11-28 20:41:42,788 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW01trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW01trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW01trimY_2P.fastq.gz [2022-11-28 20:41:46,029 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW01trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW01trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW01trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW01trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW01trimY_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 63986 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 63986 [FLASH] Combined pairs: 63115 [FLASH] Innie pairs: 63089 (99.96% of combined) [FLASH] Outie pairs: 26 (0.04% of combined) [FLASH] Uncombined pairs: 871 [FLASH] Percent combined: 98.64% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.232 seconds elapsed [2022-11-28 20:41:46,029 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW02trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW02trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW02trimY_2P.fastq.gz [2022-11-28 20:41:51,306 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW02trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW02trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW02trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW02trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW02trimY_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 123842 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 123842 [FLASH] Combined pairs: 122754 [FLASH] Innie pairs: 122715 (99.97% of combined) [FLASH] Outie pairs: 39 (0.03% of combined) [FLASH] Uncombined pairs: 1088 [FLASH] Percent combined: 99.12% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.267 seconds elapsed [2022-11-28 20:41:51,306 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW03trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW03trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW03trimY_2P.fastq.gz [2022-11-28 20:41:53,721 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW03trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW03trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW03trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW03trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW03trimY_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 51504 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 51504 [FLASH] Combined pairs: 50733 [FLASH] Innie pairs: 50717 (99.97% of combined) [FLASH] Outie pairs: 16 (0.03% of combined) [FLASH] Uncombined pairs: 771 [FLASH] Percent combined: 98.50% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 2.405 seconds elapsed [2022-11-28 20:41:53,721 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW04trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW04trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW04trimY_2P.fastq.gz [2022-11-28 20:41:55,231 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW04trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW04trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW04trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW04trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW04trimY_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 29415 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 29415 [FLASH] Combined pairs: 28354 [FLASH] Innie pairs: 28351 (99.99% of combined) [FLASH] Outie pairs: 3 (0.01% of combined) [FLASH] Uncombined pairs: 1061 [FLASH] Percent combined: 96.39% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 1.501 seconds elapsed [2022-11-28 20:41:55,231 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW05trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW05trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW05trimY_2P.fastq.gz [2022-11-28 20:42:00,565 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW05trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW05trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW05trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW05trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW05trimY_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 118524 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 118524 [FLASH] Combined pairs: 117388 [FLASH] Innie pairs: 117364 (99.98% of combined) [FLASH] Outie pairs: 24 (0.02% of combined) [FLASH] Uncombined pairs: 1136 [FLASH] Percent combined: 99.04% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.324 seconds elapsed [2022-11-28 20:42:00,565 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW06trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW06trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW06trimY_2P.fastq.gz [2022-11-28 20:42:04,517 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW06trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW06trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW06trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW06trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW06trimY_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 98476 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 98476 [FLASH] Combined pairs: 97851 [FLASH] Innie pairs: 97827 (99.98% of combined) [FLASH] Outie pairs: 24 (0.02% of combined) [FLASH] Uncombined pairs: 625 [FLASH] Percent combined: 99.37% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.943 seconds elapsed [2022-11-28 20:42:04,517 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW07trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW07trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW07trimY_2P.fastq.gz [2022-11-28 20:42:10,300 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW07trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW07trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW07trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW07trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW07trimY_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 126165 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 126165 [FLASH] Combined pairs: 124784 [FLASH] Innie pairs: 124750 (99.97% of combined) [FLASH] Outie pairs: 34 (0.03% of combined) [FLASH] Uncombined pairs: 1381 [FLASH] Percent combined: 98.91% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.772 seconds elapsed [2022-11-28 20:42:10,300 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW08trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW08trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW08trimY_2P.fastq.gz [2022-11-28 20:42:18,456 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW08trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW08trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW08trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW08trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW08trimY_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 187468 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 187468 [FLASH] Combined pairs: 186020 [FLASH] Innie pairs: 185907 (99.94% of combined) [FLASH] Outie pairs: 113 (0.06% of combined) [FLASH] Uncombined pairs: 1448 [FLASH] Percent combined: 99.23% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.146 seconds elapsed [2022-11-28 20:42:18,457 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW09trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW09trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW09trimY_2P.fastq.gz [2022-11-28 20:42:24,168 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW09trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW09trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW09trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW09trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW09trimY_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 129933 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 129933 [FLASH] Combined pairs: 128724 [FLASH] Innie pairs: 128684 (99.97% of combined) [FLASH] Outie pairs: 40 (0.03% of combined) [FLASH] Uncombined pairs: 1209 [FLASH] Percent combined: 99.07% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.701 seconds elapsed [2022-11-28 20:42:24,168 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW10trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW10trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW10trimY_2P.fastq.gz [2022-11-28 20:42:30,831 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW10trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW10trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW10trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW10trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW10trimY_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 142474 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 142474 [FLASH] Combined pairs: 141067 [FLASH] Innie pairs: 140993 (99.95% of combined) [FLASH] Outie pairs: 74 (0.05% of combined) [FLASH] Uncombined pairs: 1407 [FLASH] Percent combined: 99.01% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.652 seconds elapsed [2022-11-28 20:42:30,831 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW11trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW11trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW11trimY_2P.fastq.gz [2022-11-28 20:42:36,404 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW11trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW11trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW11trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW11trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW11trimY_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 115678 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 115678 [FLASH] Combined pairs: 114216 [FLASH] Innie pairs: 114157 (99.95% of combined) [FLASH] Outie pairs: 59 (0.05% of combined) [FLASH] Uncombined pairs: 1462 [FLASH] Percent combined: 98.74% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.563 seconds elapsed [2022-11-28 20:42:36,404 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW12trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW12trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW12trimY_2P.fastq.gz [2022-11-28 20:42:43,845 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW12trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW12trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW12trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW12trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW12trimY_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 163096 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 163096 [FLASH] Combined pairs: 161552 [FLASH] Innie pairs: 161468 (99.95% of combined) [FLASH] Outie pairs: 84 (0.05% of combined) [FLASH] Uncombined pairs: 1544 [FLASH] Percent combined: 99.05% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.430 seconds elapsed [2022-11-28 20:42:43,845 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW13trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW13trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW13trimY_2P.fastq.gz [2022-11-28 20:42:52,255 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW13trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW13trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW13trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW13trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW13trimY_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 181922 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 181922 [FLASH] Combined pairs: 180467 [FLASH] Innie pairs: 180361 (99.94% of combined) [FLASH] Outie pairs: 106 (0.06% of combined) [FLASH] Uncombined pairs: 1455 [FLASH] Percent combined: 99.20% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 8.400 seconds elapsed [2022-11-28 20:42:52,255 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW14trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW14trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW14trimY_2P.fastq.gz [2022-11-28 20:42:59,967 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW14trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW14trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW14trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW14trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW14trimY_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 169548 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 169548 [FLASH] Combined pairs: 168126 [FLASH] Innie pairs: 168069 (99.97% of combined) [FLASH] Outie pairs: 57 (0.03% of combined) [FLASH] Uncombined pairs: 1422 [FLASH] Percent combined: 99.16% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.702 seconds elapsed [2022-11-28 20:42:59,967 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW15trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW15trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW15trimY_2P.fastq.gz [2022-11-28 20:43:06,165 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW15trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW15trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW15trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW15trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW15trimY_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 133324 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 133324 [FLASH] Combined pairs: 132083 [FLASH] Innie pairs: 132030 (99.96% of combined) [FLASH] Outie pairs: 53 (0.04% of combined) [FLASH] Uncombined pairs: 1241 [FLASH] Percent combined: 99.07% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.188 seconds elapsed [2022-11-28 20:43:06,165 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW16trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW16trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW16trimY_2P.fastq.gz [2022-11-28 20:43:12,083 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW16trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW16trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW16trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW16trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW16trimY_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 132581 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 132581 [FLASH] Combined pairs: 131418 [FLASH] Innie pairs: 131338 (99.94% of combined) [FLASH] Outie pairs: 80 (0.06% of combined) [FLASH] Uncombined pairs: 1163 [FLASH] Percent combined: 99.12% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.908 seconds elapsed [2022-11-28 20:43:12,083 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW17trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW17trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW17trimY_2P.fastq.gz [2022-11-28 20:43:15,646 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW17trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW17trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW17trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW17trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW17trimY_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 74623 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 74623 [FLASH] Combined pairs: 73192 [FLASH] Innie pairs: 73171 (99.97% of combined) [FLASH] Outie pairs: 21 (0.03% of combined) [FLASH] Uncombined pairs: 1431 [FLASH] Percent combined: 98.08% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.553 seconds elapsed [2022-11-28 20:43:15,646 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW18trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW18trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW18trimY_2P.fastq.gz [2022-11-28 20:43:26,140 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW18trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW18trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW18trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW18trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW18trimY_merged.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Min overlap outie: 35 [FLASH] Max overlap: 315 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 16 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 16 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 225000 read pairs [FLASH] Processed 243211 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 243211 [FLASH] Combined pairs: 241574 [FLASH] Innie pairs: 241510 (99.97% of combined) [FLASH] Outie pairs: 64 (0.03% of combined) [FLASH] Uncombined pairs: 1637 [FLASH] Percent combined: 99.33% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 10.484 seconds elapsed [2022-11-28 20:43:26,140 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW19trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW19trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW19trimY_2P.fastq.gz [2022-11-28 20:43:33,516 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW19trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW19trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW19trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW19trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW19trimY_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 169407 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 169407 [FLASH] Combined pairs: 167978 [FLASH] Innie pairs: 167929 (99.97% of combined) [FLASH] Outie pairs: 49 (0.03% of combined) [FLASH] Uncombined pairs: 1429 [FLASH] Percent combined: 99.16% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.365 seconds elapsed [2022-11-28 20:43:33,516 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW20trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW20trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW20trimY_2P.fastq.gz [2022-11-28 20:43:39,368 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW20trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW20trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW20trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW20trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW20trimY_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 128355 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 128355 [FLASH] Combined pairs: 127089 [FLASH] Innie pairs: 127034 (99.96% of combined) [FLASH] Outie pairs: 55 (0.04% of combined) [FLASH] Uncombined pairs: 1266 [FLASH] Percent combined: 99.01% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.841 seconds elapsed [2022-11-28 20:43:39,368 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW21trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW21trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW21trimY_2P.fastq.gz [2022-11-28 20:43:45,996 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW21trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW21trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW21trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW21trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW21trimY_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 149953 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 149953 [FLASH] Combined pairs: 148738 [FLASH] Innie pairs: 148667 (99.95% of combined) [FLASH] Outie pairs: 71 (0.05% of combined) [FLASH] Uncombined pairs: 1215 [FLASH] Percent combined: 99.19% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.617 seconds elapsed [2022-11-28 20:43:45,996 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW22trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW22trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW22trimY_2P.fastq.gz [2022-11-28 20:43:50,751 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW22trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW22trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW22trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW22trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW22trimY_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 97029 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 97029 [FLASH] Combined pairs: 95939 [FLASH] Innie pairs: 95892 (99.95% of combined) [FLASH] Outie pairs: 47 (0.05% of combined) [FLASH] Uncombined pairs: 1090 [FLASH] Percent combined: 98.88% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 4.745 seconds elapsed [2022-11-28 20:43:50,751 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW23trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW23trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW23trimY_2P.fastq.gz [2022-11-28 20:43:54,499 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW23trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW23trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW23trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW23trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW23trimY_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 84685 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 84685 [FLASH] Combined pairs: 84040 [FLASH] Innie pairs: 84017 (99.97% of combined) [FLASH] Outie pairs: 23 (0.03% of combined) [FLASH] Uncombined pairs: 645 [FLASH] Percent combined: 99.24% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 3.738 seconds elapsed [2022-11-28 20:43:54,500 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW24trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW24trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW24trimY_2P.fastq.gz [2022-11-28 20:44:01,667 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW24trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW24trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW24trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW24trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW24trimY_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 160708 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 160708 [FLASH] Combined pairs: 159368 [FLASH] Innie pairs: 159281 (99.95% of combined) [FLASH] Outie pairs: 87 (0.05% of combined) [FLASH] Uncombined pairs: 1340 [FLASH] Percent combined: 99.17% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.158 seconds elapsed [2022-11-28 20:44:01,668 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW25trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW25trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW25trimY_2P.fastq.gz [2022-11-28 20:44:06,785 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW25trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW25trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW25trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW25trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW25trimY_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 112315 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 112315 [FLASH] Combined pairs: 111319 [FLASH] Innie pairs: 111304 (99.99% of combined) [FLASH] Outie pairs: 15 (0.01% of combined) [FLASH] Uncombined pairs: 996 [FLASH] Percent combined: 99.11% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.107 seconds elapsed [2022-11-28 20:44:06,785 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW26trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW26trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW26trimY_2P.fastq.gz [2022-11-28 20:44:13,247 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW26trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW26trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW26trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW26trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW26trimY_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 144399 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 144399 [FLASH] Combined pairs: 143205 [FLASH] Innie pairs: 143162 (99.97% of combined) [FLASH] Outie pairs: 43 (0.03% of combined) [FLASH] Uncombined pairs: 1194 [FLASH] Percent combined: 99.17% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.452 seconds elapsed [2022-11-28 20:44:13,247 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW27trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW27trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW27trimY_2P.fastq.gz [2022-11-28 20:44:18,985 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW27trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW27trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW27trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW27trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW27trimY_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 121139 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 121139 [FLASH] Combined pairs: 119861 [FLASH] Innie pairs: 119800 (99.95% of combined) [FLASH] Outie pairs: 61 (0.05% of combined) [FLASH] Uncombined pairs: 1278 [FLASH] Percent combined: 98.95% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.727 seconds elapsed [2022-11-28 20:44:18,985 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW28trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW28trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW28trimY_2P.fastq.gz [2022-11-28 20:44:25,307 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW28trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW28trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW28trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW28trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW28trimY_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 130197 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 130197 [FLASH] Combined pairs: 128739 [FLASH] Innie pairs: 128630 (99.92% of combined) [FLASH] Outie pairs: 109 (0.08% of combined) [FLASH] Uncombined pairs: 1458 [FLASH] Percent combined: 98.88% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.312 seconds elapsed [2022-11-28 20:44:25,307 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW29trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW29trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW29trimY_2P.fastq.gz [2022-11-28 20:44:30,880 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW29trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW29trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW29trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW29trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW29trimY_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 121664 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 121664 [FLASH] Combined pairs: 120623 [FLASH] Innie pairs: 120566 (99.95% of combined) [FLASH] Outie pairs: 57 (0.05% of combined) [FLASH] Uncombined pairs: 1041 [FLASH] Percent combined: 99.14% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.563 seconds elapsed [2022-11-28 20:44:30,880 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW30trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW30trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW30trimY_2P.fastq.gz [2022-11-28 20:44:37,099 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW30trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW30trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW30trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW30trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW30trimY_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 138614 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 138614 [FLASH] Combined pairs: 137397 [FLASH] Innie pairs: 137345 (99.96% of combined) [FLASH] Outie pairs: 52 (0.04% of combined) [FLASH] Uncombined pairs: 1217 [FLASH] Percent combined: 99.12% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.209 seconds elapsed [2022-11-28 20:44:37,099 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW31trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW31trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW31trimY_2P.fastq.gz [2022-11-28 20:44:38,843 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW31trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW31trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW31trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW31trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW31trimY_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 35068 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 35068 [FLASH] Combined pairs: 33506 [FLASH] Innie pairs: 33505 (100.00% of combined) [FLASH] Outie pairs: 1 (0.00% of combined) [FLASH] Uncombined pairs: 1562 [FLASH] Percent combined: 95.55% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 1.734 seconds elapsed [2022-11-28 20:44:38,843 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW32trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW32trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW32trimY_2P.fastq.gz [2022-11-28 20:44:45,046 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW32trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW32trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW32trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW32trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW32trimY_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 141487 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 141487 [FLASH] Combined pairs: 140271 [FLASH] Innie pairs: 140202 (99.95% of combined) [FLASH] Outie pairs: 69 (0.05% of combined) [FLASH] Uncombined pairs: 1216 [FLASH] Percent combined: 99.14% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.192 seconds elapsed [2022-11-28 20:44:45,046 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW33trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW33trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW33trimY_2P.fastq.gz [2022-11-28 20:44:51,591 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW33trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW33trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW33trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW33trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW33trimY_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 148606 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 148606 [FLASH] Combined pairs: 147387 [FLASH] Innie pairs: 147312 (99.95% of combined) [FLASH] Outie pairs: 75 (0.05% of combined) [FLASH] Uncombined pairs: 1219 [FLASH] Percent combined: 99.18% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.535 seconds elapsed [2022-11-28 20:44:51,592 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW34trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW34trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW34trimY_2P.fastq.gz [2022-11-28 20:44:57,846 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW34trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW34trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW34trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW34trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW34trimY_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 136212 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 136212 [FLASH] Combined pairs: 134959 [FLASH] Innie pairs: 134897 (99.95% of combined) [FLASH] Outie pairs: 62 (0.05% of combined) [FLASH] Uncombined pairs: 1253 [FLASH] Percent combined: 99.08% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 6.244 seconds elapsed [2022-11-28 20:44:57,847 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW35trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW35trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW35trimY_2P.fastq.gz [2022-11-28 20:45:05,012 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW35trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW35trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW35trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW35trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW35trimY_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 163029 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 163029 [FLASH] Combined pairs: 161819 [FLASH] Innie pairs: 161767 (99.97% of combined) [FLASH] Outie pairs: 52 (0.03% of combined) [FLASH] Uncombined pairs: 1210 [FLASH] Percent combined: 99.26% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 7.155 seconds elapsed [2022-11-28 20:45:05,012 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW36trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW36trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW36trimY_2P.fastq.gz [2022-11-28 20:45:10,702 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW36trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW36trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW36trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW36trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW36trimY_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 119092 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 119092 [FLASH] Combined pairs: 117998 [FLASH] Innie pairs: 117964 (99.97% of combined) [FLASH] Outie pairs: 34 (0.03% of combined) [FLASH] Uncombined pairs: 1094 [FLASH] Percent combined: 99.08% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 5.679 seconds elapsed [2022-11-28 20:45:10,702 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW37trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW37trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW37trimY_2P.fastq.gz [2022-11-28 20:45:10,750 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW37trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW37trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW37trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW37trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW37trimY_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 551 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 551 [FLASH] Combined pairs: 51 [FLASH] Innie pairs: 51 (100.00% of combined) [FLASH] Outie pairs: 0 (0.00% of combined) [FLASH] Uncombined pairs: 500 [FLASH] Percent combined: 9.26% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 0.039 seconds elapsed [2022-11-28 20:45:10,750 - INFO] Trying to run: flash2 --min-overlap=10 --max-overlap=315 --min-overlap-outie=35 --max-mismatch-density=0.25 -o JW38trimY_merged -d /nephele_data/outputs/merged/ /nephele_data/outputs/qtrimmed_seqs/JW38trimY_1P.fastq.gz /nephele_data/outputs/qtrimmed_seqs/JW38trimY_2P.fastq.gz [2022-11-28 20:45:10,793 - INFO] [FLASH] Starting FLASH v2.2.00 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW38trimY_1P.fastq.gz [FLASH] /nephele_data/outputs/qtrimmed_seqs/JW38trimY_2P.fastq.gz [FLASH] [FLASH] Output files: [FLASH] /nephele_data/outputs/merged//JW38trimY_merged.extendedFrags.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimY_merged.notCombined_1.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimY_merged.notCombined_2.fastq.gz [FLASH] /nephele_data/outputs/merged//JW38trimY_merged.hist [FLASH] /nephele_data/outputs/merged//JW38trimY_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 529 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 529 [FLASH] Combined pairs: 67 [FLASH] Innie pairs: 67 (100.00% of combined) [FLASH] Outie pairs: 0 (0.00% of combined) [FLASH] Uncombined pairs: 462 [FLASH] Percent combined: 12.67% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v2.2.00 complete! [FLASH] 0.036 seconds elapsed [2022-11-28 20:45:10,793 - INFO] Finished paired end merging. [2022-11-28 20:45:10,793 - INFO] Trying to link hist files for multiqc analysis. [2022-11-28 20:45:10,794 - INFO] Finished linking. [2022-11-28 20:45:10,794 - INFO] Trying to run multiqc on /nephele_data/outputs/multiqc_input/. [2022-11-28 20:45:10,794 - INFO] Linking logfile to multiqc inputs directory, /nephele_data/outputs/multiqc_input/. [2022-11-28 20:45:10,795 - INFO] Finished linking. [2022-11-28 20:45:23,390 - INFO] /// MultiQC 🔍 | v1.13.dev0 | multiqc | Report title: EM-v4 | 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/EM-v4_multiqc_report.html | multiqc | Data : nephele_data/outputs/EM-v4_multiqc_report_data | multiqc | MultiQC complete [2022-11-28 20:45:23,390 - INFO] Finished multiqc. [2022-11-28 20:45:23,390 - INFO] QC pipeline complete. [2022-11-28 20:45:23,390 - INFO] 0