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linguoliang / puzzle-hi-c

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subprocess.CalledProcessError #6

Open PengfeiInTuebingen opened 1 month ago

PengfeiInTuebingen commented 1 month ago

Hi, Thanks for developing this tool, i was trying to run this pipeline, i run juicer pipeline with my draft geneme first, then i used "merged_nodups.txt" for puzzle, I got an issue when doing the 9th interaction: Reach the best with 7 Iterations Traceback (most recent call last): File "/ebio/abt5_projects/3D_genome_of_brown_algae/data/software/puzzle-hi-c/main.py", line 1770, in subprocess.run("rm {0}".format(contact_file.format(iteration - 1)), shell=True, check=True, File "/ebio/abt5_projects/3D_genome_of_brown_algae/data/software/envs/odp/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'rm Chordaria_7.txt' returned non-zero exit status 1. the command I used is: "python3 /ebio/abt5_projects/3D_genome_of_brown_algae/data/software/puzzle-hi-c/main.py -c 27 -p Chordaria -s 10000 -t 0.35 -i 6 -m ../aligned/merged_nodups.txt -f ../Chordaria-linearis.fa -j /ebio/abt5_projects/software/code/miniconda3/envs/Hi-C_scaffolding/bin/juicer_tools -n 35" Do you have solution for this? Best, Pengfei

linguoliang commented 1 month ago

Hi, Thanks for developing this tool, i was trying to run this pipeline, i run juicer pipeline with my draft geneme first, then i used "merged_nodups.txt" for puzzle, I got an issue when doing the 9th interaction: Reach the best with 7 Iterations Traceback (most recent call last): File "/ebio/abt5_projects/3D_genome_of_brown_algae/data/software/puzzle-hi-c/main.py", line 1770, in subprocess.run("rm {0}".format(contact_file.format(iteration - 1)), shell=True, check=True, File "/ebio/abt5_projects/3D_genome_of_brown_algae/data/software/envs/odp/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'rm Chordaria_7.txt' returned non-zero exit status 1. the command I used is: "python3 /ebio/abt5_projects/3D_genome_of_brown_algae/data/software/puzzle-hi-c/main.py -c 27 -p Chordaria -s 10000 -t 0.35 -i 6 -m ../aligned/merged_nodups.txt -f ../Chordaria-linearis.fa -j /ebio/abt5_projects/software/code/miniconda3/envs/Hi-C_scaffolding/bin/juicer_tools -n 35" Do you have solution for this? Best, Pengfei

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