Star Index Issues To The Step 4

I am trying to index a reference genome on a pipeline with snakemake and I made this rule: rule reference_faidx_star: input: '../resources/reference/Qrob_PM1N.fa' o

Solution 1:

This problem has nothing to do with neither Snakemake, nor Python. The log clearly shows you the exact command that bash executes while Snakemake runs the pipeline:

STAR --runMode genomeGenerate --runThreadN1--genomeDir ../resources/reference/ref/ --genomeFastaFiles ../resources/reference/Qrob_PM1N.fa--sjdbGTFfile ../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf--sjdbOverhang149--genomeSAindexNbases12 -limitGenomeGenerateRAM 25000000000

Something went wrong during the execution, and that may be insufficient memory, disk problems, etc. Try to run this command in bash and check the return code: that may give you more information of what had happened.

One useful Snakemake lifehack is to use --printshellcmds flag: this would explicitly show you all commands that Snakemake runs. You may repeat these commands manually, leaving all temporary files, and locate the problem.