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Nextomics / nextsv

MIT License
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Next SV raise error on 'samtools sort' #16

Open LYC-vio opened 2 years ago

LYC-vio commented 2 years ago 
Traceback (most recent call last):
  File "/data/Softwares/nextsv/nextsv2.py", line 554, in <module>
    main()
  File "/data/Softwares/nextsv/nextsv2.py", line 128, in main
    check_samtools_version(settings)
  File "/data/Softwares/nextsv/nextsv2.py", line 254, in check_samtools_version
RuntimeError: command '/home/.conda/envs/nextsv/bin/samtools sort' return with error (code 1): samtools sort: failed to read header from "-"

seems that the error was caused by subprocess.check_output, or is it because my samtools version is not right?

I'm using samtools 1.14, and GCC/10.2.0