novitch / retrieve_sequences_fasta Goto Github PK

Hello.
I've tried unsuccessfully to run the script retrieve_sequences_fasta.pl as a slurm batch job. I'm not a bioinformatician and so think I may have misunderstood something in the readme file. But, the error message also suggests samtools/1.3 is having difficulty with the script. Any help would be appreciated.

The meat of the commands looks like this:

module load perl/5.18.4-threads
module load samtools/1.3

cp path/RSEM.isoforms.test $rundir
cp path/Trinity.fasta $rundir
cp path/retrieve_sequences_from_fasta.pl $rundir
perl retrieve_sequences_from_fasta.pl -infile=RSEM.isoforms.test -seq=Trinity.fasta -geneIDtype=simple -out=retrieve.0403.trimtrinity.fasta"

[NOTE: The RSEM.isoforms.test file is a tab-delimited file consisting of a single column of isoform names to be recovered from the Trinity.fasta file.]

The error message is as follows:
"
cat: invalid option -- 'i'
Try 'cat --help' for more information.
faidx: invalid option -- 's'

Usage: samtools faidx <file.fa|file.fa.gz> [ [...]]

Error, cmd: /opt/packages/samtools/1.3/bin/samtools faidx -seq=Trinity.fasta died with ret 65280 at retrieve_sequences_from_fasta.pl line 27.
"

Thanks for your help.