when haplotypecaller runs in batch mode, it get errors, as below
singularity exec --nv clara-parabricks_4.0.1-1.sif pbrun haplotypecaller --batch --ref ref.fa --in-bam /data/bam/ --out-variants /date/gvcf/ --gvcf
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[E::hts_hopen] Failed to open file /data/bam/
[E::hts_open_format] Failed to open file “/data/bam/” : Is a directory
samtools view: failed to open “/data/bam/” for reading: Is a directory
[E::hts_hopen] Failed to open file /data/bam/
[E::hts_open_format] Failed to open file “/data/bam/” : Is a directory
samtools view: failed to open “/data/bam/” for reading: Is a directory
/usr/local/parabricks/binaries//bin/htvc /data/ref.fa /data/bam/ 2 -o /data/gvcf -nt 5
[PB Info 2023-Jul-03 00:37:15] ------------------------------------------------------------------------------
[PB Info 2023-Jul-03 00:37:15] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Jul-03 00:37:15] || Version 4.0.1-1 ||
[PB Info 2023-Jul-03 00:37:15] || GPU-GATK4 HaplotypeCaller ||
[PB Info 2023-Jul-03 00:37:15] ------------------------------------------------------------------------------
[PB Error 2023-Jul-03 00:37:15][src/haplotype_vc.cpp:854] Expected file “/data/bam/” to be of type bam, cram or text, exiting.