Unfortunately, I'm having an issue with the pipeline that seems to be getting stuck during preprocessing. I'm not sure if it is related to this issue, but I thought I should create another issue just in case.
To test the pipeline I'm only running on set of R1/R2 read files for one sample, and it seems to be getting stuck at the SortMeRNA stage. I've included the traceback error, but I'm not able to figure out what the error refers to.
File "/home/ctrivedi/miniconda3/envs/mosca/share/MOSCA/scripts/mosca_tools.py", line 24, in run_command
check=True)
File "/home/ctrivedi/miniconda3/envs/mosca/lib/python3.7/subprocess.py", line
512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['sortmerna', '--ref', 'resources_directory/rRNA_databases/silva-arc-23s-id98.fasta,resources_directory/rRNA_databases/silva-arc-23s-id98.idx:resources_directory/rRNA_databases/rfam-5s-database-id98.fasta,resources_directory/rRNA_databases/rfam-5s-database-id98.idx:resources_directory/rRNA_databases/silva-euk-18s-id95.fasta,resources_directory/rRNA_databases/silva-euk-18s-id95.idx:resources_directory/rRNA_databases/rfam-5.8s-database-id98.fasta,resources_directory/rRNA_databases/rfam-5.8s-database-id98.idx:resources_directory/rRNA_databases/silva-bac-23s-id98.fasta,resources_directory/rRNA_databases/silva-bac-23s-id98.idx:resources_directory/rRNA_databases/silva-bac-16s-id90.fasta,resources_directory/rRNA_databases/silva-bac-16s-id90.idx:resources_directory/rRNA_databases/silva-euk-28s-id98.fasta,resources_directory/rRNA_databases/silva-euk-28s-id98.idx:resources_directory/rRNA_databases/silva-arc-16s-id95.fasta,resources_directory/rRNA_databases/silva-arc-16s-id95.idx', '--reads', 'output/Preprocess/SortMeRNA/MIT1_interleaved.fastq', '--aligned', 'output/Preprocess/SortMeRNA/MIT1_accepted', '--fastx', '--other', 'output/Preprocess/SortMeRNA/MIT1_rejected', '-a', '24', '--paired_out']' returned non-zero exit status 1.
[Sun May 2 16:58:42 2021]
Error in rule preprocess:
jobid: 0
output: output/Preprocess/Trimmomatic/quality_trimmed_MIT1_forward_paired.fq, output/Preprocess/Trimmomatic/quality_trimmed_MIT1_reverse_paired.fq
RuleException:
CalledProcessError in line 111 of /home/ctrivedi/miniconda3/envs/mosca/share/MOSCA/scripts/Snakefile:
Command 'set -euo pipefail; python /home/ctrivedi/miniconda3/envs/mosca/share/MOSCA/scripts/preprocess.py -i Raw/RNA_TR_zymo11_S6_R1_001.fastq,Raw/RNA_TR_zymo11_S6_R2_001.fastq -t 24 -o output/Preprocess -adaptdir resources_directory/adapters -rrnadbs resources_directory/rRNA_databases -d mrna -rd resources_directory -n MIT1 --minlen 100 --avgqual 20' returned non-zero exit status 1.
File "/home/ctrivedi/miniconda3/envs/mosca/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 2352, in run_wrapper
File "/home/ctrivedi/miniconda3/envs/mosca/share/MOSCA/scripts/Snakefile", line 111, in __rule_preprocess
File "/home/ctrivedi/miniconda3/envs/mosca/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 569, in _callback
File "/home/ctrivedi/miniconda3/envs/mosca/lib/python3.7/concurrent/futures/thread.py", line 57, in run
File "/home/ctrivedi/miniconda3/envs/mosca/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 555, in cached_or_run
File "/home/ctrivedi/miniconda3/envs/mosca/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 2364, in run_wrapper
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/ctrivedi/Working/Deep_Purple/GR19_Metatranscriptomes/Mosca/.snakemake/log/2021-05-02T165747.387856.snakemake.log
I'm using the default config file, and I've included my experiments file (as txt as github doesn't seem to support tsv upload). Any information would be greatly appreciated. Thanks in advance for any help.