MOSCA issueshttps://gitlab.bio.di.uminho.pt/iquasere/MOSCA/-/issues2021-03-09T02:48:31Zhttps://gitlab.bio.di.uminho.pt/iquasere/MOSCA/-/issues/14No such file or directory: 'output/Preprocess/SortMeRNA/read1.txt'2021-03-09T02:48:31ZJoão SequeiraNo 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 wil...*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 <module>
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