When using the fq2bam function, is there an option to simply skip a line rather than report an error when a format issue is encountered in the Fastq file? On one hand, discarding all reads due to a single line error is not ideal, especially when data is limited. On the other hand, during batch processing, I have to delete the problematic Fastq file and rerun the program each time. Could you let me know if such an option already exists or if it might be added in the future? (I noticed that when I process the same Fastq file using bwa, no errors are reported, which makes me curious about the differences between the two tools.) By the way, your tool is truly excellent!
here are the error message:
Command error:
processing SRR15970750.bam
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /GSE184427/SRR15970750.fastq.gz
[Parabricks Options Mesg]: @RG\tID:SRR15970750.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:SRR15970750.1.1
[PB Info 2025-Jan-02 07:52:55] ------------------------------------------------------------------------------
[PB Info 2025-Jan-02 07:52:55] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2025-Jan-02 07:52:55] || Version 4.4.0-1 ||
[PB Info 2025-Jan-02 07:52:55] || GPU-PBBWA mem, Sorting Phase-I ||
[PB Info 2025-Jan-02 07:52:55] ------------------------------------------------------------------------------
[PB Info 2025-Jan-02 07:52:55] Mode = single-ended-gpu
[PB Info 2025-Jan-02 07:52:55] Running with 1 GPU(s), using 4 stream(s) per device with 16 worker threads per GPU
[PB Info 2025-Jan-02 07:53:05] # 0 0 0 0 bases/GPU/minute: 0.0
[PB Info 2025-Jan-02 07:53:15] # 10 10 0 893502885 bases/GPU/minute: 5361017310.0
[PB Info 2025-Jan-02 07:53:25] # 0 0 0 1855151584 bases/GPU/minute: 5769892194.0
[PB Info 2025-Jan-02 07:53:35] # 0 0 0 2073453296 bases/GPU/minute: 1309810272.0
[PB Info 2025-Jan-02 07:53:45] # 0 0 0 2271226427 bases/GPU/minute: 1186638786.0
[PB Info 2025-Jan-02 07:53:55] # 0 0 0 2618974900 bases/GPU/minute: 2086490838.0
[PB Info 2025-Jan-02 07:54:05] # 6 0 0 3130351653 bases/GPU/minute: 3068260518.0
[PB Error 2025-Jan-02 07:54:05][src/PBFastqFile.cpp:148] Improperly formatted FASTQ file. ID line did not start with ‘@’ on line 126854249, exiting.
For technical support visit NVIDIA Clara - NVIDIA Docs
Exiting…
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
Could not run fq2bam
Exiting pbrun …