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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Input BAM file not found #394

Open espelpz opened 4 months ago

espelpz commented 4 months ago

Hi,

I am trying to run lumpyexpress but I am getting the following error despite the bam file exists and the path is correct:

(base) elpz@picasso:/mnt/scratch/users/b02_cimes_uma/elpz/SVs_manta_normal/021LH19/manta_normal/manta_results> lumpyexpress -B /mnt2/fscratch/users/b02_cimes_uma/elpz/lhodgkin_try3/021LH19/results/8_applybqsr/0/021LH19/0_021LH19.bam Sourcing executables from /usr/local/bin/lumpyexpress.config ...

Checking for required python modules (python)...

usage: lumpyexpress [options]

options: -B FILE full BAM or CRAM file(s) (comma separated) (required) -S FILE split reads BAM file(s) (comma separated) -D FILE discordant reads BAM files(s) (comma separated) -R FILE indexed reference genome fasta file (recommended for CRAMs)

 -d FILE  bedpe file of depths (comma separated and prefixed by sample:)
          e.g sample_x:/path/to/sample_x.bedpe,sample_y:/path/to/sample_y.bedpe
 -o FILE  output file [fullBam.bam.vcf]
 -x FILE  BED file to exclude
 -P       output probability curves for each variant
 -m INT   minimum sample weight for a call [4]
 -r FLOAT trim threshold [0]
 -T DIR   temp directory [./output_prefix.XXXXXXXXXXXX]
 -k       keep temporary files

 -K FILE  path to lumpyexpress.config file
            (default: same directory as lumpyexpress)
 -v       verbose
 -h       show this message

Error: file /mnt2/fscratch/users/b02_cimes_uma/elpz/lhodgkin_try3/021LH19/results/8_applybqsr/0/021LH19/0_021LH19.bam not found.

real 0m0,492s user 0m0,263s sys 0m0,188s

How may I fix this?

Thank you in advance!

Cheers,

Espe