Input fastq file have different size, How to slove it?

[fan724963]

Hi!
I use fq2bam , it have this error when it run a few time .

It is my command :docker run --gpus 2 --rm --volume /data3/wangxx/F9fsw_raw/:/1 --volume /data3/wangxxref/:/2 --volume /data3/wangxx/output/:/3 nvcr.io/nvidia/clara/clara-parabricks:4.1.1-1 pbrun fq2bam --ref /2/q94.genome.fasta --in-fq /1/F9fsw_raw-1.clean.fastq /1/F9fsw_raw-2.clean.fastq --out-bam /3/F9fsw_vsq94.bam

The error is :
[PB Info 2024-Jan-11 05:51:48] 421135680 62980000000
[PB Info 2024-Jan-11 05:51:58] 426149090 63740000000
[PB Info 2024-Jan-11 05:52:09] 431162616 64500000000
[PB Info 2024-Jan-11 05:52:20] 436176088 65240000000
[PB Info 2024-Jan-11 05:52:30] 441189488 66010000000
[PB Info 2024-Jan-11 05:52:41] 446203274 66740000000
[PB Error 2024-Jan-11 05:52:47][src/PBFastqFile.cpp:283] Input files/1/F9fsw_raw-1.clean.fastq and /1/F9fsw_raw-2.clean.fastq have different sizes, exiting.
CUDA error at ParaBricks/inc/driverAPIs.h:233 code=4() “cuGraphLaunch(graghExec_, reinterpret_cast(stream))”
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Could not run fq2bam
Exiting pbrun …

How to slove this problem.
Thank you!

[tongz]

Hi,

For the pair-ended input, you need to make sure that the number of records should be the same in these 2 fastq files. If not then probably you want to truncate one of them.