[2023-04-01 12:59:25,990 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.23.4, tag: Nephele_2023_March_28, commit: d9e1ff4
[2023-04-01 12:59:25,991 - INFO] Python version: 3.8.13
[2023-04-01 12:59:25,991 - INFO] Current time: 2023-04-01 12:59
[2023-04-01 12:59:25,991 - INFO] Pipeline name: QC Reads
[2023-04-01 12:59:26,229 - INFO] Job Description: E23-ITS
[2023-04-01 12:59:26,229 - INFO] Job parameters
job_id: 0c661a97049a
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: None
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
[2023-04-01 12:59:26,229 - INFO] Checking Mapfile for Gzipped inputs.
[2023-04-01 12:59:26,230 - INFO] Gzipped files listed in map file, attempting to rm .gz extension.
[2023-04-01 12:59:26,230 - INFO] Done. Attempting file decompression.
[2023-04-01 12:59:30,894 - INFO] Finished decompression.
[2023-04-01 12:59:30,894 - INFO] Skipping FASTQ file validation
[2023-04-01 12:59:30,894 - INFO] Starting pipe...
[2023-04-01 12:59:30,904 - INFO] Trying to generate samples
[2023-04-01 12:59:30,904 - INFO] Starting Fastqc, outputs in /nephele_data/outputs/multiqc_input/.
[2023-04-01 12:59:30,905 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-10_S50_L001_R1_001.fastq
[2023-04-01 12:59:35,395 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-11_S51_L001_R1_001.fastq
[2023-04-01 12:59:38,631 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-12_S52_L001_R1_001.fastq
[2023-04-01 12:59:41,866 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-13_S53_L001_R1_001.fastq
[2023-04-01 12:59:45,102 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-14_S54_L001_R1_001.fastq
[2023-04-01 12:59:48,403 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-15_S55_L001_R1_001.fastq
[2023-04-01 12:59:51,635 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-16_S56_L001_R1_001.fastq
[2023-04-01 12:59:54,908 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-17_S57_L001_R1_001.fastq
[2023-04-01 12:59:57,147 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-18_S58_L001_R1_001.fastq
[2023-04-01 13:00:00,406 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-19_S59_L001_R1_001.fastq
[2023-04-01 13:00:03,636 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-1_S41_L001_R1_001.fastq
[2023-04-01 13:00:05,868 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-20_S60_L001_R1_001.fastq
[2023-04-01 13:00:09,104 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-21_S61_L001_R1_001.fastq
[2023-04-01 13:00:12,334 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-22_S62_L001_R1_001.fastq
[2023-04-01 13:00:15,563 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-23_S63_L001_R1_001.fastq
[2023-04-01 13:00:18,798 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-24_S64_L001_R1_001.fastq
[2023-04-01 13:00:22,026 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-25_S65_L001_R1_001.fastq
[2023-04-01 13:00:24,260 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-26_S66_L001_R1_001.fastq
[2023-04-01 13:00:27,491 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-27_S67_L001_R1_001.fastq
[2023-04-01 13:00:30,722 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-28_S68_L001_R1_001.fastq
[2023-04-01 13:00:33,963 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-29_S69_L001_R1_001.fastq
[2023-04-01 13:00:37,193 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-2_S42_L001_R1_001.fastq
[2023-04-01 13:00:40,427 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-30_S70_L001_R1_001.fastq
[2023-04-01 13:00:43,659 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-31_S71_L001_R1_001.fastq
[2023-04-01 13:00:47,890 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-32_S72_L001_R1_001.fastq
[2023-04-01 13:00:51,125 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-33_S73_L001_R1_001.fastq
[2023-04-01 13:00:54,359 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-34_S74_L001_R1_001.fastq
[2023-04-01 13:00:57,594 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-35_S75_L001_R1_001.fastq
[2023-04-01 13:01:00,825 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-36_S76_L001_R1_001.fastq
[2023-04-01 13:01:04,054 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-37_S77_L001_R1_001.fastq
[2023-04-01 13:01:07,282 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-38_S78_L001_R1_001.fastq
[2023-04-01 13:01:10,577 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-3_S43_L001_R1_001.fastq
[2023-04-01 13:01:13,809 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-4_S44_L001_R1_001.fastq
[2023-04-01 13:01:17,043 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-5_S45_L001_R1_001.fastq
[2023-04-01 13:01:20,278 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-6_S46_L001_R1_001.fastq
[2023-04-01 13:01:23,515 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-7_S47_L001_R1_001.fastq
[2023-04-01 13:01:26,754 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-8_S48_L001_R1_001.fastq
[2023-04-01 13:01:28,992 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-9_S49_L001_R1_001.fastq
[2023-04-01 13:01:32,227 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-NTC1_S79_L001_R1_001.fastq
[2023-04-01 13:01:35,537 - INFO] trying to run:
fastqc -o /nephele_data/outputs/multiqc_input/ /nephele_data/inputs/E23-ITS-NTC2_S80_L001_R1_001.fastq
[2023-04-01 13:01:38,772 - INFO] Finished Fastqc, see /nephele_data/outputs/multiqc_input/ for outputs.
[2023-04-01 13:01:38,782 - INFO] cutadapt args: ['--cores', 16, '--match-read-wildcards', '--overlap', 3, '--error-rate', 0.1, '-g', 'ACCTGCGGARGGATCA']
[2023-04-01 13:01:38,782 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-10_S50_L001_R1_001.fastq
[2023-04-01 13:01:39,153 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-11_S51_L001_R1_001.fastq
[2023-04-01 13:01:39,449 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-12_S52_L001_R1_001.fastq
[2023-04-01 13:01:39,788 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-13_S53_L001_R1_001.fastq
[2023-04-01 13:01:40,098 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-14_S54_L001_R1_001.fastq
[2023-04-01 13:01:40,457 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-15_S55_L001_R1_001.fastq
[2023-04-01 13:01:40,738 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-16_S56_L001_R1_001.fastq
[2023-04-01 13:01:40,943 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-17_S57_L001_R1_001.fastq
[2023-04-01 13:01:41,065 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-18_S58_L001_R1_001.fastq
[2023-04-01 13:01:41,340 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-19_S59_L001_R1_001.fastq
[2023-04-01 13:01:41,576 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-1_S41_L001_R1_001.fastq
[2023-04-01 13:01:41,696 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-20_S60_L001_R1_001.fastq
[2023-04-01 13:01:42,060 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-21_S61_L001_R1_001.fastq
[2023-04-01 13:01:42,414 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-22_S62_L001_R1_001.fastq
[2023-04-01 13:01:42,838 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-23_S63_L001_R1_001.fastq
[2023-04-01 13:01:43,185 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-24_S64_L001_R1_001.fastq
[2023-04-01 13:01:43,454 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-25_S65_L001_R1_001.fastq
[2023-04-01 13:01:43,570 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-26_S66_L001_R1_001.fastq
[2023-04-01 13:01:44,135 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-27_S67_L001_R1_001.fastq
[2023-04-01 13:01:44,464 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-28_S68_L001_R1_001.fastq
[2023-04-01 13:01:44,815 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-29_S69_L001_R1_001.fastq
[2023-04-01 13:01:45,123 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-2_S42_L001_R1_001.fastq
[2023-04-01 13:01:45,429 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-30_S70_L001_R1_001.fastq
[2023-04-01 13:01:45,840 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-31_S71_L001_R1_001.fastq
[2023-04-01 13:01:46,136 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-32_S72_L001_R1_001.fastq
[2023-04-01 13:01:46,322 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-33_S73_L001_R1_001.fastq
[2023-04-01 13:01:46,446 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-34_S74_L001_R1_001.fastq
[2023-04-01 13:01:46,615 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-35_S75_L001_R1_001.fastq
[2023-04-01 13:01:46,962 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-36_S76_L001_R1_001.fastq
[2023-04-01 13:01:47,485 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-37_S77_L001_R1_001.fastq
[2023-04-01 13:01:47,967 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-38_S78_L001_R1_001.fastq
[2023-04-01 13:01:48,616 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-3_S43_L001_R1_001.fastq
[2023-04-01 13:01:48,929 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-4_S44_L001_R1_001.fastq
[2023-04-01 13:01:49,253 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-5_S45_L001_R1_001.fastq
[2023-04-01 13:01:49,579 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-6_S46_L001_R1_001.fastq
[2023-04-01 13:01:50,041 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-7_S47_L001_R1_001.fastq
[2023-04-01 13:01:50,352 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-8_S48_L001_R1_001.fastq
[2023-04-01 13:01:50,470 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-9_S49_L001_R1_001.fastq
[2023-04-01 13:01:50,592 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-NTC1_S79_L001_R1_001.fastq
[2023-04-01 13:01:51,279 - INFO] Running cutadapt for: /nephele_data/inputs/E23-ITS-NTC2_S80_L001_R1_001.fastq
[2023-04-01 13:01:51,741 - INFO] Finished cutadapt.
[2023-04-01 13:01:51,741 - INFO] Run Trimmomatic quality trimming selected.
[2023-04-01 13:01:51,741 - INFO] Trying to create /nephele_data/outputs/qtrimmed_seqs/.
[2023-04-01 13:01:51,751 - 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
[2023-04-01 13:01:52,807 - 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

[2023-04-01 13:01:52,807 - 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
[2023-04-01 13:01:53,671 - 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

[2023-04-01 13:01:53,671 - 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
[2023-04-01 13:01:54,720 - 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

[2023-04-01 13:01:54,720 - 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
[2023-04-01 13:01:55,593 - 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

[2023-04-01 13:01:55,593 - 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
[2023-04-01 13:01:56,767 - 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

[2023-04-01 13:01:56,767 - 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
[2023-04-01 13:01:57,613 - 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

[2023-04-01 13:01:57,613 - 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
[2023-04-01 13:01:58,065 - 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

[2023-04-01 13:01:58,065 - 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
[2023-04-01 13:01:58,245 - 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

[2023-04-01 13:01:58,245 - 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
[2023-04-01 13:01:59,059 - 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

[2023-04-01 13:01:59,059 - 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
[2023-04-01 13:01:59,640 - 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

[2023-04-01 13:01:59,640 - 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
[2023-04-01 13:01:59,791 - 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

[2023-04-01 13:01:59,791 - 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
[2023-04-01 13:02:00,929 - 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

[2023-04-01 13:02:00,929 - 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
[2023-04-01 13:02:01,917 - 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

[2023-04-01 13:02:01,917 - 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
[2023-04-01 13:02:03,258 - 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

[2023-04-01 13:02:03,258 - 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
[2023-04-01 13:02:04,304 - 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

[2023-04-01 13:02:04,304 - 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
[2023-04-01 13:02:04,992 - 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

[2023-04-01 13:02:04,992 - 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
[2023-04-01 13:02:05,151 - 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

[2023-04-01 13:02:05,151 - 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
[2023-04-01 13:02:07,218 - 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

[2023-04-01 13:02:07,218 - 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
[2023-04-01 13:02:08,176 - 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

[2023-04-01 13:02:08,176 - 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
[2023-04-01 13:02:09,252 - 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

[2023-04-01 13:02:09,252 - 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
[2023-04-01 13:02:10,216 - 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

[2023-04-01 13:02:10,216 - 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
[2023-04-01 13:02:11,133 - 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

[2023-04-01 13:02:11,133 - 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
[2023-04-01 13:02:12,568 - 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

[2023-04-01 13:02:12,568 - 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
[2023-04-01 13:02:13,440 - 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

[2023-04-01 13:02:13,440 - 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
[2023-04-01 13:02:13,819 - 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

[2023-04-01 13:02:13,820 - 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
[2023-04-01 13:02:14,021 - 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

[2023-04-01 13:02:14,021 - 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
[2023-04-01 13:02:14,352 - 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

[2023-04-01 13:02:14,352 - 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
[2023-04-01 13:02:15,529 - 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

[2023-04-01 13:02:15,529 - 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
[2023-04-01 13:02:17,264 - 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

[2023-04-01 13:02:17,264 - 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
[2023-04-01 13:02:18,826 - 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

[2023-04-01 13:02:18,826 - 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
[2023-04-01 13:02:21,418 - 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

[2023-04-01 13:02:21,418 - 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
[2023-04-01 13:02:22,303 - 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

[2023-04-01 13:02:22,303 - 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
[2023-04-01 13:02:23,347 - 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

[2023-04-01 13:02:23,347 - 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
[2023-04-01 13:02:24,360 - 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

[2023-04-01 13:02:24,360 - 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
[2023-04-01 13:02:25,944 - 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

[2023-04-01 13:02:25,944 - 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
[2023-04-01 13:02:26,853 - 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

[2023-04-01 13:02:26,853 - 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
[2023-04-01 13:02:27,006 - 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

[2023-04-01 13:02:27,006 - 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
[2023-04-01 13:02:27,214 - 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

[2023-04-01 13:02:27,214 - 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
[2023-04-01 13:02:29,956 - 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

[2023-04-01 13:02:29,956 - 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
[2023-04-01 13:02:31,458 - 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

[2023-04-01 13:02:31,458 - INFO] Quality trimming complete, see /nephele_data/outputs/multiqc_input/trimmo.log.
[2023-04-01 13:02:31,458 - INFO] Trying to run multiqc on /nephele_data/outputs/multiqc_input/.
[2023-04-01 13:02:31,458 - INFO] Linking logfile to multiqc inputs directory, /nephele_data/outputs/multiqc_input/.
[2023-04-01 13:02:31,458 - INFO] Finished linking.

[2023-04-01 13:02:40,260 - INFO] 
  /// MultiQC 🔍 | v1.13.dev0

|           multiqc | MultiQC Version v1.14 now available!
|           multiqc | Report title: E23-ITS
|           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-ITS_multiqc_report.html
|           multiqc | Data        : nephele_data/outputs/E23-ITS_multiqc_report_data
|           multiqc | MultiQC complete

[2023-04-01 13:02:40,260 - INFO] Finished multiqc.

[2023-04-01 13:02:40,260 - INFO] QC pipeline complete.
[2023-04-01 13:02:40,260 - INFO] 0