fetchdata.py / SOAPFuse issue

[DiprimaSa]

Dear EasyFuse Software Developers, I am writing to seek your assistance regarding an issue I am facing while using the EasyFuse software.

I encountered a problem that I have been unable to resolve on my own. In several instances (though not always, on some of my samples the software runs just fine), when running the software with the containers, it produces the following error message:       Error: Command "['/code/miniconda3/bin/python', '/code/easyfuse/fetchdata.py', '-i', '/output/Sample_S4_L002', '-o', '/output/Sample_S4_L002/fetchdata', '-s', '1153_ESOCA12T_S4_L002', '-c', '/code/easyfuse/config.ini', '--fq1', '/output/Sample_S4_L002/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz', '--fq2', '/output/Sample_S4_L002/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz', '--fusion_support', '1']" returned non-zero exit status

After careful investigation, I believe the problem might be related to the output generated by the SOAPFuse tool, which seems to be incomplete. In particular, I discovered that the issue could be caused by failure of one of the scripts located in the following directory: EasyFuse_out/Sample_name/Sample_name/fusion/soapfuse/TEMP/config_shell.1684889656_400/

The script is called "fusion.s08.sh", the log of which (08.sh.log) contains the following message: flow-ends-at-s08-normally_SF_INFO_FD2_fusion_result_is_empty

If I understand correctly what happens, the reason why EasyFuse then terminates is that the python script fetchdata.py does not find the expected output from SOAPFuse.

I have reviewed the software's documentation and searched for solutions online but, unfortunately, I have been unable to find a resolution to this problem. Therefore, I would greatly appreciate if you could provide me with some guidance or assistance in resolving this issue.

I include the following details that may help you zoom in on what the problem might be: EasyFuse software version: 1.3.7 Script to reproduce the issue:       #SBATCH --job-name=EasyFuse_${subfolder_name}       #SBATCH --partition=workq       #SBATCH --account=diprima.santo       #SBATCH --mem=40GB       #SBATCH --time=INFINITE       #SBATCH --cpus-per-task=8       #SBATCH --mail-type=ALL       #SBATCH --error="${subfolder_name}.err"       #SBATCH --output="${subfolder_name}.out"

      singularity exec --containall --bind "$reference_annotation:/ref" --bind "$subfolder:/data" --bind "$out_dir/$subfolder_name:/output" docker://tronbioinformatics/easyfuse:lates       t python /code/easyfuse/processing.py -i /data/ -o /output

If there are any logs or error reports that I can share with you to assist in diagnosing the issue, please let me know and I will gladly provide them to you.

Thank you for your attention to this matter. I appreciate your expertise and the efforts you put into developing this software and I thank you for making it freely available to the community.

[Shiyanth]

I am having the exact same issue. I was wondering if you were able to debug this at any point?

[sunqiangzai]

I am running into the same issue. I was wondering if you were able to debug this at any point.

[ibn-salem]

Thanks for pointing this out. Can you confirm that this issue occurs with the latest EasyFuse version?