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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Input BAM not recognized #653

Closed espelpz closed 6 months ago

espelpz commented 9 months ago

Hi,

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

(base) elpz@picasso:/mnt2/fscratch/users/b02_cimes_uma/elpz/lhodgkin_try3/014LH19/results/8_applybqsr/0/014LH19> gridss -r /mnt/home/users/b02_cimes_uma/elpz/genomas_ref/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta -o 014LH19_gridss_all_calls.vcf /mnt2/fscratch/users/b02_cimes_uma/elpz/lhodgkin_try3/014LH19/results/8_applybqsr/0/014LH19/0_014LH19.bam /mnt2/fscratch/users/b02_cimes_uma/elpz/lhodgkin_try3/014LH19/results/8_applybqsr/1/014LH19/1_014LH19.bam Using working directory "." Wed Feb 21 13:56:45 CET 2024: Full log file is: ./gridss.full.20240221_135645.picasso.12919.log Wed Feb 21 13:56:45 CET 2024: Found /usr/bin/time /usr/bin/time: unrecognized option '--verbose' BusyBox v1.32.1 (2021-04-13 11:15:36 UTC) multi-call binary.

Usage: time [-vpa] [-o FILE] PROG ARGS

Run PROG, display resource usage when it exits

-v Verbose -p POSIX output format -f FMT Custom format -o FILE Write result to FILE -a Append (else overwrite) Wed Feb 21 13:56:45 CET 2024: Using GRIDSS jar /usr/local/share/gridss-2.13.2-2/gridss.jar Wed Feb 21 13:56:45 CET 2024: Using reference genome "/mnt/home/users/b02_cimes_uma/elpz/genomas_ref/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta" Wed Feb 21 13:56:45 CET 2024: Using output VCF 014LH19_gridss_all_calls.vcf Wed Feb 21 13:56:45 CET 2024: Using assembly bam 014LH19_gridss_all_calls.vcf.assembly.bam Wed Feb 21 13:56:45 CET 2024: Using 8 worker threads. Wed Feb 21 13:56:45 CET 2024: Using no blacklist bed. The encode DAC blacklist is recommended for hg19. Wed Feb 21 13:56:45 CET 2024: Using JVM maximum heap size of 30g for assembly and variant calling. Wed Feb 21 13:56:46 CET 2024: Input file /mnt2/fscratch/users/b02_cimes_uma/elpz/lhodgkin_try3/014LH19/results/8_applybqsr/0/014LH19/0_014LH19.bam does not exist "exit $EX_NOINPUT" command completed with exit code 66.

The underlying error message can be found in ./gridss.full.20240221_135645.picasso.12919.log

real 0m2,804s user 0m3,728s sys 0m10,912s

How may I fix this?

Thank you in advance!

Cheers,

Espe

d-cameron commented 6 months ago

Wed Feb 21 13:56:45 CET 2024: Found /usr/bin/time /usr/bin/time: unrecognized option '--verbose'

Not sure what your OS is but the root cause is that your version of /usr/bin/time does not support the --verbose command-line parameter. The workaround is to update/install a time version that supports --verbose. One such workaround is to use the conda time package https://anaconda.org/conda-forge/time