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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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[INFO][Launcher]biostar139647 Exited with failure (-1) #237

Open tbazilegith opened 1 year ago

tbazilegith commented 1 year ago

Verify

Module installed in cluster java/1.8.0_31 3) jvarkit/20180405

Subject of the issue

I want to convert a fasta alignment into bam command used: biostar139647 aln_dir/lp_allstrains03.aln -o aln_dir/lp_allstrains03.bam --samoutputformat BAM

Your environment

Steps to reproduce

Tell us how to reproduce this issue. Please provide an example.

Actual behaviour

[INFO][Launcher]biostar139647 Exited with failure (-1)

lindenb commented 1 year ago

Hi,

biostar139647 ...

this is not the correct way to run the command. It should be something like java -jar jvarkit.jar biostar139647 .... see the documentation. https://jvarkit.readthedocs.io/en/latest/Biostar139647/

if it still fails, please provide a minimal set of files to reproduce the problem.