[2023-04-02 00:07:09,747 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.23.4, tag: Nephele_2023_March_28, commit: d9e1ff4
[2023-04-02 00:07:09,747 - INFO] Python version: 3.8.13
[2023-04-02 00:07:09,747 - INFO] Current time: 2023-04-02 00:07
[2023-04-02 00:07:09,747 - INFO] Pipeline name: QC Reads
[2023-04-02 00:07:09,984 - INFO] Job Description: E23-ITSpreprocess2
[2023-04-02 00:07:09,985 - INFO] Job parameters
job_id: 8da5d7441e43
inputs_dir: None
outputs_dir: None
map_file: <_io.TextIOWrapper name='/nephele_data/inputs/E23-ITS_QC_pipeline_template_single_end_N2_corrected.txt' mode='r' encoding='UTF-8'>
data_type: SE
run_cutadapt: True
error_rate: 0.1
indels: True
overlap: 3
match_read_wildcards: True
match_adapter_wildcards: True
adapter_f: AACTTTYARCAAYGGATCTCCTGTCTCTTATACACATCTCCGAGCCCACGAGAC
adapter_r: None
front_f: ACCTGCGGARGGATCA
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: False
f2_min_overlap: 10
f2_max_overlap: 315
f2_min_overlap_outie: 35
f2_max_mismatch_density: 0.25
[2023-04-02 00:07:09,985 - INFO] Checking Mapfile for Gzipped inputs.
[2023-04-02 00:07:09,985 - INFO] Gzipped files listed in map file, attempting to rm .gz extension.
[2023-04-02 00:07:09,985 - INFO] Done. Attempting file decompression.
[2023-04-02 00:07:14,625 - INFO] Finished decompression.
[2023-04-02 00:07:14,625 - INFO] Skipping FASTQ file validation
[2023-04-02 00:07:14,625 - INFO] Starting pipe...
[2023-04-02 00:07:14,634 - INFO] Trying to generate samples
[2023-04-02 00:07:14,634 - INFO] Starting Fastqc, outputs in /nephele_data/outputs/multiqc_input/.
[2023-04-02 00:07:14,635 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-10_S50_L001_R1_001.fastq
[2023-04-02 00:07:18,139 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-11_S51_L001_R1_001.fastq
[2023-04-02 00:07:21,366 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-12_S52_L001_R1_001.fastq
[2023-04-02 00:07:24,663 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-13_S53_L001_R1_001.fastq
[2023-04-02 00:07:27,892 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-14_S54_L001_R1_001.fastq
[2023-04-02 00:07:31,119 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-15_S55_L001_R1_001.fastq
[2023-04-02 00:07:34,345 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-16_S56_L001_R1_001.fastq
[2023-04-02 00:07:37,572 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-17_S57_L001_R1_001.fastq
[2023-04-02 00:07:39,800 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-18_S58_L001_R1_001.fastq
[2023-04-02 00:07:43,026 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-19_S59_L001_R1_001.fastq
[2023-04-02 00:07:46,252 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-1_S41_L001_R1_001.fastq
[2023-04-02 00:07:48,475 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-20_S60_L001_R1_001.fastq
[2023-04-02 00:07:51,700 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-21_S61_L001_R1_001.fastq
[2023-04-02 00:07:54,929 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-22_S62_L001_R1_001.fastq
[2023-04-02 00:07:58,155 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-23_S63_L001_R1_001.fastq
[2023-04-02 00:08:01,383 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-24_S64_L001_R1_001.fastq
[2023-04-02 00:08:04,611 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-25_S65_L001_R1_001.fastq
[2023-04-02 00:08:06,838 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-26_S66_L001_R1_001.fastq
[2023-04-02 00:08:10,075 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-27_S67_L001_R1_001.fastq
[2023-04-02 00:08:13,354 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-28_S68_L001_R1_001.fastq
[2023-04-02 00:08:16,583 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-29_S69_L001_R1_001.fastq
[2023-04-02 00:08:19,827 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-2_S42_L001_R1_001.fastq
[2023-04-02 00:08:23,056 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-30_S70_L001_R1_001.fastq
[2023-04-02 00:08:26,285 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-31_S71_L001_R1_001.fastq
[2023-04-02 00:08:29,511 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-32_S72_L001_R1_001.fastq
[2023-04-02 00:08:32,739 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-33_S73_L001_R1_001.fastq
[2023-04-02 00:08:35,966 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-34_S74_L001_R1_001.fastq
[2023-04-02 00:08:38,193 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-35_S75_L001_R1_001.fastq
[2023-04-02 00:08:41,460 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-36_S76_L001_R1_001.fastq
[2023-04-02 00:08:44,687 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-37_S77_L001_R1_001.fastq
[2023-04-02 00:08:47,945 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-38_S78_L001_R1_001.fastq
[2023-04-02 00:08:51,244 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-3_S43_L001_R1_001.fastq
[2023-04-02 00:08:54,471 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-4_S44_L001_R1_001.fastq
[2023-04-02 00:08:57,699 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-5_S45_L001_R1_001.fastq
[2023-04-02 00:09:00,928 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-6_S46_L001_R1_001.fastq
[2023-04-02 00:09:04,157 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-7_S47_L001_R1_001.fastq
[2023-04-02 00:09:07,386 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-8_S48_L001_R1_001.fastq
[2023-04-02 00:09:09,661 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-9_S49_L001_R1_001.fastq
[2023-04-02 00:09:12,889 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-NTC1_S79_L001_R1_001.fastq
[2023-04-02 00:09:17,117 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-NTC2_S80_L001_R1_001.fastq
[2023-04-02 00:09:20,346 - INFO] Finished Fastqc, see /nephele_data/outputs/multiqc_input/ for outputs.
[2023-04-02 00:09:20,356 - INFO] cutadapt args: ['--cores', 16, '--match-read-wildcards', '--overlap', 3, '--error-rate', 0.1, '-a', 'AACTTTYARCAAYGGATCTCCTGTCTCTTATACACATCTCCGAGCCCACGAGAC', '-g', 'ACCTGCGGARGGATCA']
[2023-04-02 00:09:20,356 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-10_S50_L001_R1_001.fastq
[2023-04-02 00:09:20,813 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-11_S51_L001_R1_001.fastq
[2023-04-02 00:09:21,189 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-12_S52_L001_R1_001.fastq
[2023-04-02 00:09:21,596 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-13_S53_L001_R1_001.fastq
[2023-04-02 00:09:21,991 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-14_S54_L001_R1_001.fastq
[2023-04-02 00:09:22,418 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-15_S55_L001_R1_001.fastq
[2023-04-02 00:09:22,769 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-16_S56_L001_R1_001.fastq
[2023-04-02 00:09:23,048 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-17_S57_L001_R1_001.fastq
[2023-04-02 00:09:23,169 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-18_S58_L001_R1_001.fastq
[2023-04-02 00:09:23,520 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-19_S59_L001_R1_001.fastq
[2023-04-02 00:09:23,827 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-1_S41_L001_R1_001.fastq
[2023-04-02 00:09:23,945 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-20_S60_L001_R1_001.fastq
[2023-04-02 00:09:24,380 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-21_S61_L001_R1_001.fastq
[2023-04-02 00:09:24,820 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-22_S62_L001_R1_001.fastq
[2023-04-02 00:09:25,336 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-23_S63_L001_R1_001.fastq
[2023-04-02 00:09:25,761 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-24_S64_L001_R1_001.fastq
[2023-04-02 00:09:26,114 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-25_S65_L001_R1_001.fastq
[2023-04-02 00:09:26,230 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-26_S66_L001_R1_001.fastq
[2023-04-02 00:09:26,910 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-27_S67_L001_R1_001.fastq
[2023-04-02 00:09:27,321 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-28_S68_L001_R1_001.fastq
[2023-04-02 00:09:27,746 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-29_S69_L001_R1_001.fastq
[2023-04-02 00:09:28,129 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-2_S42_L001_R1_001.fastq
[2023-04-02 00:09:28,516 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-30_S70_L001_R1_001.fastq
[2023-04-02 00:09:29,025 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-31_S71_L001_R1_001.fastq
[2023-04-02 00:09:29,391 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-32_S72_L001_R1_001.fastq
[2023-04-02 00:09:29,643 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-33_S73_L001_R1_001.fastq
[2023-04-02 00:09:29,766 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-34_S74_L001_R1_001.fastq
[2023-04-02 00:09:29,981 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-35_S75_L001_R1_001.fastq
[2023-04-02 00:09:30,403 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-36_S76_L001_R1_001.fastq
[2023-04-02 00:09:31,011 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-37_S77_L001_R1_001.fastq
[2023-04-02 00:09:31,589 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-38_S78_L001_R1_001.fastq
[2023-04-02 00:09:32,349 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-3_S43_L001_R1_001.fastq
[2023-04-02 00:09:32,746 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-4_S44_L001_R1_001.fastq
[2023-04-02 00:09:33,146 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-5_S45_L001_R1_001.fastq
[2023-04-02 00:09:33,554 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-6_S46_L001_R1_001.fastq
[2023-04-02 00:09:34,107 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-7_S47_L001_R1_001.fastq
[2023-04-02 00:09:34,490 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-8_S48_L001_R1_001.fastq
[2023-04-02 00:09:34,605 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-9_S49_L001_R1_001.fastq
[2023-04-02 00:09:34,725 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-NTC1_S79_L001_R1_001.fastq
[2023-04-02 00:09:35,531 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-NTC2_S80_L001_R1_001.fastq
[2023-04-02 00:09:36,081 - INFO] Finished cutadapt.
[2023-04-02 00:09:36,081 - INFO] Run Trimmomatic quality trimming selected.
[2023-04-02 00:09:36,081 - INFO] Trying to create /nephele_data/outputs/qtrimmed_seqs/.
[2023-04-02 00:09:36,091 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-10_S50_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-10.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:37,152 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-10_S50_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-10.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 25797 Surviving: 25753 (99.83%) Dropped: 44 (0.17%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:37,152 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-11_S51_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-11.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:38,009 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-11_S51_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-11.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 21199 Surviving: 21167 (99.85%) Dropped: 32 (0.15%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:38,009 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-12_S52_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-12.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:39,058 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-12_S52_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-12.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 29281 Surviving: 29240 (99.86%) Dropped: 41 (0.14%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:39,058 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-13_S53_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-13.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:39,924 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-13_S53_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-13.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 19795 Surviving: 19757 (99.81%) Dropped: 38 (0.19%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:39,924 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-14_S54_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-14.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:41,097 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-14_S54_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-14.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 32990 Surviving: 32930 (99.82%) Dropped: 60 (0.18%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:41,097 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-15_S55_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-15.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:41,915 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-15_S55_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-15.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 21236 Surviving: 21183 (99.75%) Dropped: 53 (0.25%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:41,915 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-16_S56_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-16.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:42,350 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-16_S56_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-16.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 5617 Surviving: 5606 (99.80%) Dropped: 11 (0.20%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:42,350 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-17_S57_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-17.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:42,524 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-17_S57_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-17.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 203 Surviving: 203 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:42,524 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-18_S58_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-18.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:43,303 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-18_S58_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-18.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 19004 Surviving: 18960 (99.77%) Dropped: 44 (0.23%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:43,303 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-19_S59_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-19.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:43,882 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-19_S59_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-19.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 11987 Surviving: 11949 (99.68%) Dropped: 38 (0.32%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:43,882 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-1_S41_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-1.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:44,030 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-1_S41_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-1.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 6 Surviving: 6 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:44,030 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-20_S60_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-20.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:45,161 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-20_S60_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-20.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 30676 Surviving: 30612 (99.79%) Dropped: 64 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:45,161 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-21_S61_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-21.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:46,126 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-21_S61_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-21.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 23488 Surviving: 23409 (99.66%) Dropped: 79 (0.34%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:46,127 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-22_S62_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-22.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:47,454 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-22_S62_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-22.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 35779 Surviving: 35705 (99.79%) Dropped: 74 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:47,455 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-23_S63_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-23.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:48,470 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-23_S63_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-23.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 26120 Surviving: 26064 (99.79%) Dropped: 56 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:48,470 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-24_S64_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-24.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:49,170 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-24_S64_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-24.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 15120 Surviving: 15088 (99.79%) Dropped: 32 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:49,170 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-25_S65_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-25.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:49,325 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-25_S65_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-25.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 30 Surviving: 30 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:49,325 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-26_S66_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-26.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:51,371 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-26_S66_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-26.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 57577 Surviving: 57453 (99.78%) Dropped: 124 (0.22%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:51,372 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-27_S67_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-27.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:52,310 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-27_S67_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-27.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 22845 Surviving: 22790 (99.76%) Dropped: 55 (0.24%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:52,310 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-28_S68_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-28.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:53,353 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-28_S68_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-28.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 28556 Surviving: 28497 (99.79%) Dropped: 59 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:53,353 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-29_S69_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-29.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:54,342 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-29_S69_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-29.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 25198 Surviving: 25169 (99.88%) Dropped: 29 (0.12%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:54,343 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-2_S42_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-2.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:55,240 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-2_S42_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-2.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 22466 Surviving: 22429 (99.84%) Dropped: 37 (0.16%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:55,240 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-30_S70_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-30.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:56,687 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-30_S70_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-30.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 44809 Surviving: 44712 (99.78%) Dropped: 97 (0.22%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:56,687 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-31_S71_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-31.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:57,546 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-31_S71_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-31.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 21571 Surviving: 21534 (99.83%) Dropped: 37 (0.17%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:57,546 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-32_S72_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-32.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:57,912 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-32_S72_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-32.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 5053 Surviving: 5047 (99.88%) Dropped: 6 (0.12%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:57,912 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-33_S73_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-33.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:58,118 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-33_S73_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-33.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 455 Surviving: 454 (99.78%) Dropped: 1 (0.22%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:58,118 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-34_S74_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-34.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:58,454 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-34_S74_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-34.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 3446 Surviving: 3442 (99.88%) Dropped: 4 (0.12%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:58,454 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-35_S75_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-35.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:09:59,603 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-35_S75_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-35.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 34018 Surviving: 33952 (99.81%) Dropped: 66 (0.19%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:09:59,603 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-36_S76_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-36.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:01,322 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-36_S76_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-36.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 49090 Surviving: 48951 (99.72%) Dropped: 139 (0.28%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:01,323 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-37_S77_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-37.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:02,845 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-37_S77_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-37.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 39842 Surviving: 39713 (99.68%) Dropped: 129 (0.32%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:02,845 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-38_S78_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-38.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:05,422 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-38_S78_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-38.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 80212 Surviving: 80063 (99.81%) Dropped: 149 (0.19%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:05,422 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-3_S43_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-3.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:06,291 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-3_S43_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-3.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 20479 Surviving: 20429 (99.76%) Dropped: 50 (0.24%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:06,291 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-4_S44_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-4.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:07,314 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-4_S44_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-4.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 26457 Surviving: 26411 (99.83%) Dropped: 46 (0.17%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:07,314 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-5_S45_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-5.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:08,316 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-5_S45_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-5.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 25342 Surviving: 25286 (99.78%) Dropped: 56 (0.22%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:08,316 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-6_S46_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-6.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:09,890 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-6_S46_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-6.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 44111 Surviving: 44017 (99.79%) Dropped: 94 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:09,890 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-7_S47_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-7.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:10,799 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-7_S47_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-7.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 23066 Surviving: 23036 (99.87%) Dropped: 30 (0.13%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:10,799 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-8_S48_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-8.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:10,957 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-8_S48_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-8.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 3 Surviving: 3 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:10,958 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-9_S49_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-9.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:11,161 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-9_S49_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-9.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 400 Surviving: 398 (99.50%) Dropped: 2 (0.50%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:11,161 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-NTC1_S79_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-NTC1.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:13,884 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-NTC1_S79_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-NTC1.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 83413 Surviving: 83239 (99.79%) Dropped: 174 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:13,884 - INFO] Trying to run
trimmomatic SE -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-NTC2_S80_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-NTC2.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
[2023-04-02 00:10:15,380 - INFO] TrimmomaticSE: Started with arguments:
 -threads 16 -phred33 /nephele_data/outputs/cutadapt_trimmed/E23-ITS-NTC2_S80_L001_R1_001.fastq.gz /nephele_data/outputs/qtrimmed_seqs/E23-ITS-NTC2.fastq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:30 AVGQUAL:0
Input Reads: 41264 Surviving: 41176 (99.79%) Dropped: 88 (0.21%)
TrimmomaticSE: Completed successfully

[2023-04-02 00:10:15,380 - INFO] Quality trimming complete, see /nephele_data/outputs/multiqc_input/trimmo.log.
[2023-04-02 00:10:15,380 - INFO] Trying to run multiqc on /nephele_data/outputs/multiqc_input/.
[2023-04-02 00:10:15,380 - INFO] Linking logfile to multiqc inputs directory, /nephele_data/outputs/multiqc_input/.
[2023-04-02 00:10:15,380 - INFO] Finished linking.

[2023-04-02 00:10:23,925 - INFO] 
  /// MultiQC 🔍 | v1.13.dev0

|           multiqc | MultiQC Version v1.14 now available!
|           multiqc | Report title: E23-ITSpreprocess2
|           multiqc | Search path : /nephele_data/outputs/multiqc_input
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 121/121  
|            fastqc | Found 40 reports
|          cutadapt | Found 40 reports
|       trimmomatic | Found 40 logs
|           multiqc | Compressing plot data
|           multiqc | Report      : nephele_data/outputs/E23-ITSpreprocess2_multiqc_report.html
|           multiqc | Data        : nephele_data/outputs/E23-ITSpreprocess2_multiqc_report_data
|           multiqc | MultiQC complete

[2023-04-02 00:10:23,925 - INFO] Finished multiqc.

[2023-04-02 00:10:23,925 - INFO] QC pipeline complete.
[2023-04-02 00:10:23,925 - INFO] 0