bwa index - failed to find .pac

Question

[amy__]

Hello, I am running this job on the hpc (I have not included some of the job admin before because it made the post messy, but I can post if needed:

singularity run $CONTAINER index -p Polyposis_Exome_Analysis/bwa/index/IndexedHuman_output/ Polyposis_Exome_Analysis/bwa/index/HumanRefSeq/GRCh38_latest_genomic.fa

However I keep getting this error:

  pack FASTA…[bns_fasta2bntseq] fail to open file ‘Polyposis_Exome_Analysis/bwa/index/IndexedHuman_output/.pac’: No such file or directory.

I saw another post about making sure to have permissions for the directories, which I definitely do since I made them:

ls -lh

GRCh38_latest_genomic.fa -rwxrwxr-x. 1 c.c21087028 c.c21087028 3.1G Jan 18 11.56 GRCh38_latest_genomic.fa

So I'm not entirely sure what is going wrong, thanks in advanced! Amy

Answer 1

[Pierre Lindenbaum]

try

-p Polyposis_Exome_Analysis/bwa/index/IndexedHuman_output/GRCh38_latest_genomic.fa

not

-p Polyposis_Exome_Analysis/bwa/index/IndexedHuman_output/

[amy__]

Hi Pierre,

I think you were correct, I also changed my location to avoid any errors that way:

cd /scratch/c.c21087028/Polyposis_Exome_Analysis/bwa/index/indexhumanrefseq_output/

singularity run $CONTAINER index /scratch/c.c21087028/Polyposis_Exome_Analysis/bwa/index/HumanRefSeq/GRCh38_latest_genomic.fa

I'll let you know if it works when its finished, but no errors so far.

Thanks for all your help, Amy