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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
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python: src/memory.c:244: parasail_result_new_trace: Assertion `a > 0' failed. #36

Closed charliechen912ilovbash closed 1 year ago

charliechen912ilovbash commented 1 year ago

Hello,

I am using version 0.4.0. During the nanomonsv get, it showed the following error messages. I am using 1 thread and 192Gb memory, the normal and tumor BAM files are 131Gb and 81Gb, separately. Does this mean memory is not enough?


05/17/2023 12:48:35 - nanomonsv.run - INFO - Clustering insertion type supporting reads for putative SVs
05/17/2023 12:48:42 - nanomonsv.run - INFO - Clustering deletion type supporting reads for putative SVs
05/17/2023 12:48:47 - nanomonsv.run - INFO - Gathering sequences of supporting reads
05/17/2023 13:47:27 - nanomonsv.run - INFO - Generate consensus sequences
python: src/memory.c:244: parasail_result_new_trace: Assertion `a > 0' failed.```
friend1ws commented 1 year ago

@charliechen912ilovbash Hi, did this work? I guess it happened in single breakend SV detection (--sbnd mode).

charliechen912ilovbash commented 1 year ago

Thank you for your reply. I was using FASTA (generated by SURVIVOR simreads) mapped BAM as input, could this be the reason? I found another read simulator that can generate FASTQ, and the BAM worked well with NanomonSV, so I closed the issue.

friend1ws commented 1 year ago

OK. Thanks.