Fsq2bam slowing down?

doing fastq alignment, I got message as follows:

[PB Info 2023-May-18 15:09:07] [M::runCPUThreads] read 66668 sequences (10000200 bp)…
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 27528, 2, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR…
[M::mem_pestat] (25, 50, 75) percentile: (317, 367, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (109, 629)
[M::mem_pestat] mean and std.dev: (369.16, 80.67)
[M::mem_pestat] low and high boundaries for proper pairs: (5, 733)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs

After those message, the process seems hang-up. Any hints?



Hi @wei.xing ,

Can you please let know what GPUs you are using? What is the command you tried? and what version of Parabricks you used?

And also make sure that you are not running something else on the system


hi, the issue was sorted. It was due to fastq files (generated by fastq dump), but not gpu or bam mem. Anyway, thanks for supporting.

Happy to hear that it was sorted.

Thank you

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