featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumped)"
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@07a95528
Last seen 26 days ago
China

Hello, when I was going through the last step of metagenomic data processing, featurecounts kept reporting errors, and there was no output result file. Error message displayed:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumped)"

My code is as follows: "featureCounts -T 20 -a 500cut.gtf -o 500read.count -p -B -C -f -t exon -g gene_id bwa/*.bam"

I have checked line 2890 of the bam file and I think there should be no problem with it, I don't know the cause of this error, I would appreciate it if you could help me solve it. bam file

metaMSdata • 281 views
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The error that is relevant is Aborted (core dumped). This line 2890 refers to the C source code that throws the error, it is not relevant for the end user. Aborted (core dumped) usually means that either CPU limits were exceeded or memory was short. What are your system speciications?

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Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?

Thank you for your reply.

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