FeatureCounts error
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5 months ago

Hi,

I'm trying to run FeatureCounts with my nanopore data (cDNA sequencing). I run the command:

featureCounts -g gene_id -Q 3 -a Homo_sapiens.GRCh38.97.gtf -o feature_counts_CLL-0849-02 CLL-0849-02.aligned.bam


and an error occurs:

Assertion failed: (NULL == pairer -> bam_margin_table -> appendix2), function SAM_pairer_finish_margin_table, file input-files.c, line 4612.


What does it mean? What should I do?

RNAseq • 330 views
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Sorry for my initial comment, I did not notice the input bam file was indeed present. Can you do two things: a) make sure you have the most recent version of the featureCounts and 2) be sure the BAM file is not corrupted, e.g. by running samtools quickcheck -qvvv your.bam and then posting the output?

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I have samtools 1.11. What command should I run to check my .bam files? I have tried with samtools qiuckcheck -v CLL-0849-02.aligned.bam but there is no output...

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Sorry, edited it, it is quickcheck, I had no coffee today, sorry for my poor-quality comments :)

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I appreciate your help even without coffee :) So I run the command:

samtools quickcheck -qvvv CLL-0849-02.aligned.bam

And the output looks like that:

verbosity set to 3 checking CLL-0849-02.aligned.bam opened CLL-0849-02.aligned.bam CLL-0849-02.aligned.bam is sequence data CLL-0849-02.aligned.bam has 194 targets in header. CLL-0849-02.aligned.bam has good EOF block.

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So the BAM seems ok. If you use the current version of featureCounts and the error persists you can try and drop a message in the subread google group. If possible try to provide a reproducible example, e.g. a small subset of this bam file, plus which operating system you are on and how you installed the tool. Maybe others here have better suggestions on the actual error.