Question: featureCounts error: Assertion `1 != corrected_run' failed.

Question

[giuseppe0525]

Hi,

I got an error when I tried to get gene counts from .bam files with featureCounts. The error message was: " featureCounts: input-files.c:5381: SAM_pairer_run: Assertion `1 != corrected_run' failed. task_pipeline.sh: line 460: 21820 Aborted (core dumped) featureCounts -a ${annot} -o ${ftcoutput_nstd} -g 'gene_name' -p -t exon -T 16 SRR*bam "

And I run the command "featureCounts -a ${annot} -o ${ftcoutput_nstd} -g 'gene_name' -p -t exon -T 16 SRR*bam"

There were about 50 .bam files to be processed in total. It seemed that some of them caused the error, because there's no error when I randomly picked two .bam files to run the program.

Do you have any idea what had gone wrong? Thanks.

[Michael]

Hi, I don't exactly know what 1 != corrected_run this is supposed to protect against, but from the name of the function, could it be that some bam files are paired and others not? Could the files that do not work have been truncated in some way: check out How to systematically check if a bam file is truncated also if you downloaded them, try to check md5sum or some other hash. If they all are ok, try to run the command in a for loop in bash over each file to find the offending files.

• https://groups.google.com/forum/#!topic/subread/XL1wHA3Xa4c (are you using the latest version)

[giuseppe0525]

Thank you for your suggestion. There seemed to be a bug which was fixed in the latest version. I should have stated the version of featureCounts I used.