No such file or directory: 'output/Preprocess/SortMeRNA/read1.txt'

Created by: szypanther

hi iquasere, Sorry for trouble you again, right now I testing more data by MOSCA. During the process, I encounter such error but the pipeline not stop and still continue run. Is this missing file will impact the whole process or we can ignore it?

............................ join output/Preprocess/SortMeRNA/read1.txt output/Preprocess/SortMeRNA/read2.txt | awk '{print $1" "$2"\n"$3"\n+\n"$4 > "output/Preprocess/SortMeRNA/mt3namerep_forward.fastq";print $1" "$5"\n"$6"\n+\n"$7 > "output/Preprocess/SortMeRNA/mt3namerep_reverse.fastq"}' Traceback (most recent call last): File "/media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/preprocess.py", line 379, in Preprocesser().run() File "/media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/preprocess.py", line 349, in run original_files=True if args.input == original_input else False) File "/media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/preprocess.py", line 226, in rrna_removal '{}/{}_reverse.fastq'.format(out_dir, name), out_dir) File "/media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/preprocess.py", line 191, in remove_orphans os.remove(file) FileNotFoundError: [Errno 2] No such file or directory: 'output/Preprocess/SortMeRNA/read1.txt' [Thu Mar 4 16:38:34 2021] Error in rule preprocess: jobid: 0 output: output/Preprocess/Trimmomatic/quality_trimmed_mt3name_forward_paired.fq, output/Preprocess/Trimmomatic/quality_trimmed_mt3name_reverse_paired.fq

RuleException: CalledProcessError in line 111 of /media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/Snakefile: Command 'set -euo pipefail; python /media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/preprocess.py -i /media/zyshen/MOSCA/20201023_L_QMK/mt3_R1.fastq,/media/zyshen/MOSCA/20201023_L_QMK/mt3_R2.fastq -t 10 -o output/Preprocess -adaptdir /media/zyshen/work/MOSCA/MOSCA-1.3.4/adapters -rrnadbs /media/zyshen/work/MOSCA/MOSCA-1.3.4/rRNA_databases -d mrna -rd /media/zyshen/work/MOSCA/MOSCA-1.3.4 -n mt3name --minlen 100 --avgqual 20' returned non-zero exit status 1. File "/media/zyshen/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/executors/init.py", line 2340, in run_wrapper File "/media/zyshen/work/MOSCA/MOSCA-1.3.5/workflow/Snakefile", line 111, in __rule_preprocess File "/media/zyshen/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/executors/init.py", line 568, in _callback File "/media/zyshen/miniconda3/envs/snakemake/lib/python3.6/concurrent/futures/thread.py", line 56, in run File "/media/zyshen/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/executors/init.py", line 554, in cached_or_run File "/media/zyshen/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/executors/init.py", line 2352, in run_wrapper Exiting because a job execution failed. Look above for error message Removed: output/Preprocess/SortMeRNA/mt3namerep_interleaved.fastq fastqc --outdir output/Preprocess/FastQC --threads 10 --extract output/Preprocess/SortMeRNA/mt3namerep_forward.fastq output/Preprocess/SortMeRNA/mt3namerep_reverse.fastq Started analysis of mt3namerep_forward.fastq Started analysis of mt3namerep_reverse.fastq Approx 5% complete for mt3namerep_forward.fastq Approx 5% complete for mt3namerep_reverse.fastq Approx 10% complete for mt3namerep_forward.fastq Approx 10% complete for mt3namerep_reverse.fastq Approx 15% complete for mt3namerep_forward.fastq Approx 15% complete for mt3namerep_reverse.fastq Approx 20% complete for mt3namerep_forward.fastq .......

zhiyong