Error running parabricks on gcp

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Version: common-cu121.m118
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Linux instance-20240326-211639 5.10.0-28-cloud-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64

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Last login: Wed Mar 27 00:08:08 2024 from 35.235.243.82
(base) frederick@instance-20240326-211639:~$ docker run      --rm      --gpus all      --volume `pwd`:`pwd`      --workdir `pwd`/parabricks_sample      nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1      pbrun germline      --ref Ref/Homo_sapiens_assembly38.fasta      --in-fq Data/sample_1.fq.gz Data/sample_2.fq.gz      --knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi      --out-bam output.bam      --out-variants germline.vcf      --out-recal-file recal.txt --low-memory
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation


[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /home/frederick/parabricks_sample/Data/sample_1.fq.gz and
/home/frederick/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for /home/frederick/parabricks_sample/Data/sample_1.fq.gz and
/home/frederick/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[PB Info 2024-Mar-27 00:25:02] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:25:02] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2024-Mar-27 00:25:02] ||                              Version 4.3.0-1                             ||
[PB Info 2024-Mar-27 00:25:02] ||                       GPU-BWA mem, Sorting Phase-I                       ||
[PB Info 2024-Mar-27 00:25:02] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2024-Mar-27 00:25:23] GPU-BWA mem
[PB Info 2024-Mar-27 00:25:23] ProgressMeter    Reads           Base Pairs Aligned
[PB Info 2024-Mar-27 00:25:47] 5043564          580000000
[PB Info 2024-Mar-27 00:26:09] 10087128 1160000000
[PB Info 2024-Mar-27 00:26:30] 15130692 1740000000
[PB Info 2024-Mar-27 00:26:51] 20174256 2320000000
[PB Info 2024-Mar-27 00:27:13] 25217820 2900000000
[PB Info 2024-Mar-27 00:27:34] 30261384 3480000000
[PB Info 2024-Mar-27 00:27:55] 35304948 4060000000
[PB Info 2024-Mar-27 00:28:16] 40348512 4640000000
[PB Info 2024-Mar-27 00:28:38] 45392076 5220000000
[PB Info 2024-Mar-27 00:28:59] 50435640 5800000000
[PB Info 2024-Mar-27 00:29:15] 
GPU-BWA Mem time: 232.053483 seconds
[PB Info 2024-Mar-27 00:29:15] GPU-BWA Mem is finished.

[main] CMD: /usr/local/parabricks/binaries/bin/bwa mem -Z ./pbOpts.txt -l -F 0 /home/frederick/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /home/frederick/parabricks_sample/Data/sample_1.fq.gz /home/frederick/parabricks_sample/Data/sample_2.fq.gz @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[main] Real time: 252.865 sec; CPU: 4256.537 sec
[PB Info 2024-Mar-27 00:29:15] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:15] ||        Program:                      GPU-BWA mem, Sorting Phase-I        ||
[PB Info 2024-Mar-27 00:29:15] ||        Version:                                           4.3.0-1        ||
[PB Info 2024-Mar-27 00:29:15] ||        Start Time:                       Wed Mar 27 00:25:02 2024        ||
[PB Info 2024-Mar-27 00:29:15] ||        End Time:                         Wed Mar 27 00:29:15 2024        ||
[PB Info 2024-Mar-27 00:29:15] ||        Total Time:                           4 minutes 13 seconds        ||
[PB Info 2024-Mar-27 00:29:15] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:15] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:15] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2024-Mar-27 00:29:15] ||                              Version 4.3.0-1                             ||
[PB Info 2024-Mar-27 00:29:15] ||                             Sorting Phase-II                             ||
[PB Info 2024-Mar-27 00:29:15] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:15] progressMeter - Percentage
[PB Info 2024-Mar-27 00:29:15] 0.0
[PB Info 2024-Mar-27 00:29:20] 81.5
[PB Info 2024-Mar-27 00:29:25] Sorting and Marking: 10.002 seconds
[PB Info 2024-Mar-27 00:29:25] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:25] ||        Program:                                  Sorting Phase-II        ||
[PB Info 2024-Mar-27 00:29:25] ||        Version:                                           4.3.0-1        ||
[PB Info 2024-Mar-27 00:29:25] ||        Start Time:                       Wed Mar 27 00:29:15 2024        ||
[PB Info 2024-Mar-27 00:29:25] ||        End Time:                         Wed Mar 27 00:29:25 2024        ||
[PB Info 2024-Mar-27 00:29:25] ||        Total Time:                                     10 seconds        ||
[PB Info 2024-Mar-27 00:29:25] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:25] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:25] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2024-Mar-27 00:29:25] ||                              Version 4.3.0-1                             ||
[PB Info 2024-Mar-27 00:29:25] ||                         Marking Duplicates, BQSR                         ||
[PB Info 2024-Mar-27 00:29:25] ------------------------------------------------------------------------------
[PB Info 2024-Mar-27 00:29:25] BQSR using CUDA device(s): { 0 }
[PB Info 2024-Mar-27 00:29:26] Using PBBinBamFile for BAM writing
[PB Info 2024-Mar-27 00:29:26] progressMeter -  Percentage
[PB Info 2024-Mar-27 00:29:36] 0.0
[PB Info 2024-Mar-27 00:29:46] 0.0
[PB Info 2024-Mar-27 00:29:56] 0.0
[PB Error 2024-Mar-27 00:29:58][src/PBVcfFile.cpp:336] Expecting a .vcf or .vcf.gz as file extension, exiting.
[PB Error 2024-Mar-27 00:29:58][src/main.cu:617] Logic error: Popped null BinData from delete queue., exiting.
[PB Error 2024-Mar-27 00:29:58][src/main.cu:593] Logic error: Popped null BinData off write queue., exiting.
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks
Exiting...


Could not run fq2bam as part of germline pipeline
Exiting pbrun ...
(base) frederick@instance-20240326-211639:~$

It runs just fine up until it says it is ’ Expecting a .vcf or .vcf.gz as file extension, exiting.’

Looks like you passed the tabix index (.tbi) instead of the VCF for your knownSites file - try again using the VCF?