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Illumina / paragraph

Graph realignment tools for structural variants
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Problem starting the script multigrmpy.py #77

Open aaaniich opened 1 year ago

aaaniich commented 1 year ago

Hi! I try to use this tool, but when I use this command: python3 bin/multigrmpy.py -i vvv.vcf -m manchr3.txt -r genome.fa -o test4

I have next errors:

in manifestrse the options: Unknown column read length 2023-01-19 10:05:07,167 ERROR Traceback (most recent call last): 2023-01-19 10:05:07,167 ERROR File "bin/multigrmpy.py", line 316, in run subprocess.check_call(commandline, shell=True, stderr=subprocess.STDOUT) 2023-01-19 10:05:07,167 ERROR File "/usr/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) 2023-01-19 10:05:07,167 ERROR subprocess.CalledProcessError: Command '/opt/paragraph-build/bin/grmpy --response-file=/tmp/tmpmavc_bwf.txt' returned non-zero exit status 1.

Can youexplain me, what's wrong?

mzwaig commented 1 year ago

I'm getting a similar error

Han-Cao commented 9 months ago

I also ran into this error and found it is caused by Windows line endings. You can check the manifest file and replace all '\r\n' with '\n'