Fq2bam [E::bwa_idx_load_from_disk] fail to locate the index files

[pavan_kumar.kotha]

I am trying to run fq2bam on AWS with nextflow
Container image used: nvcr.io/nvidia/clara/clara-parabricks-fq2bam:4.0.0-1
Command run:
pbrun fq2bam
–ref reference.fa
–in-fq R1.fq.gz R2.fq.gz
–out-bam out.bam

I have all the index files at the same location as the reference.fa file
reference.fa, reference.fa.fai, reference.fa.sa, reference.fa.amb, reference.fa.bwt, reference.fa.pac, reference.fa.ann

I am able run bwa-mem with the same set of fastqs, reference and index files

But I am seeing this error with pbrun: [E::bwa_idx_load_from_disk] fail to locate the index files

Could anyone help me resolve the this issue.

Thank you

Error log:
[Parabricks Options Mesg]: @RG\tID:H375CDSX5.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H375CDSX5.1
[PB Info 2023-Jul-06 09:08:44] ------------------------------------------------------------------------------
[PB Info 2023-Jul-06 09:08:44] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Jul-06 09:08:44] || Version 4.0.0-1 ||
“[PB Info 2023-Jul-06 09:08:44] || GPU-BWA mem, Sorting Phase-I ||”
[PB Info 2023-Jul-06 09:08:44] ------------------------------------------------------------------------------
[E::bwa_idx_load_from_disk] fail to locate the index files
[PB Info 2023-Jul-06 09:08:44] ------------------------------------------------------------------------------
“[PB Info 2023-Jul-06 09:08:44] || Program: GPU-BWA mem, Sorting Phase-I ||”
[PB Info 2023-Jul-06 09:08:44] || Version: 4.0.0-1 ||
[PB Info 2023-Jul-06 09:08:44] || Start Time: Thu Jul 6 09:08:44 2023 ||
[PB Info 2023-Jul-06 09:08:44] || End Time: Thu Jul 6 09:08:44 2023 ||
[PB Info 2023-Jul-06 09:08:44] || Total Time: 0 seconds ||
[PB Info 2023-Jul-06 09:08:44] ------------------------------------------------------------------------------
For technical support visit … 4.0.0/Help.html
Exiting…
Please visit … clara/#parabricks for detailed documentation
Could not run fq2bam
Exiting pbrun …

[gburnett]

Hey @pavan_kumar.kotha,

I would maybe try re-indexing the files with samtools index. I agree that it is strange, if it worked with bwa, it should work with fq2bam.

[pavan_kumar.kotha]

I found the solution here: GitHub - clara-parabricks-workflows/parabricks-nextflow: Accelerated genomics workflows in NextFlow

It worked when I passed the reference and index files as tar archive.

It turned out the issue was with AWS itself. The reference and index files were symlinks pointing to files at different locations. So pbrun couldn’t find the index files at the same absolute path as the reference.fa.