featureCounts segmentation fault

[santhilalsubhash]

subread-1.5.0-p1-source works

Thank you Wei Shi, the new patched version (subread-1.5.0-p1-source) works for these files now.

[shi]

That's great. Thanks for letting us know.

[dvanic]

Error with long CIGARs

I'm trying to map some long reads (PacBio public human data), and use featureCounts to count reads to features (there are other ways of doing this, which I also use, but I'd like to use featureCounts on both the PacBio data and some IBM data to treat both datasets consistently. However, I'm getting the following error:

WARNING: cigar string is too long to the buffer.
Please only use the compressed BAM format.
featureCounts: sambam-file.c:594: PBam_chunk_gets: Assertion `0' failed.

Can you please update featureCounts to not collapse when a CIGAR is too long?

Thanks in advance,
Darya

[shi]

What is the version of featureCounts you use?

[arkanion]

Segmentation fault (core dumped)

If I run the below command from the commandline it works fine, however it corrupts with "Segmentation fault (core dumped)" if I run within sh script:

featureCounts -T 10 -Q 10 -a library/genes.gtf -o gene_expression.txt 344/RNA-Seq/CD34_2_clean/CD34_2_clean_aligned_sorted.bam

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
	v1.5.0-p3

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P 344/RNA ... ||
||                                                                            ||
||             Output file : 344/RNA-S ... ||
||                 Summary : 344/RNA-S ... ||
||              Annotation : library/genes.gtf (GTF)            ||
||                                                                            ||
||                 Threads : 10                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file library/genes.gtf ...                   ||
||    Features : 430178                                                       ||
||    Meta-features : 23710                                                   ||
||    Chromosomes/contigs : 49                                                ||
||                                                                            ||
|| Process BAM file 344/RNA-Seq/CD34_2 ... ||
||    Paired-end reads are included.                                          ||
||    Assign fragments (read pairs) to features...                            ||
||                                                                            ||
||    WARNING: reads from the same pair were found not adjacent to each       ||
||             other in the input (due to read sorting by location or         ||
||             reporting of multi-mapping read pairs).                        ||
||                                                                            ||
||    Read re-ordering is performed.                                          ||
||                                                                            ||
Segmentation fault (core dumped)

Apparently the patch does not work on my system.

Is there any clever fix yet?

[dvanic]

What is the version of featureCounts you use?

Rsubread_1.20.6 or command line version subread-1.5.0-p1-Linux-x86_64

[shi]

Can you update to Subread 1.5.1 and try again?

[hbrugge]

I'm also getting a segmentation error.

I use featureCount on 33k files and only 3 of them return this error. I'm getting no stdout or err on these 3 files, just:
44818 Segmentation fault (core dumped)

The query I use:
featureCounts -s 1 -T 8 -t exon -g gene_id -a Homo_sapiens.GRCh37.75.gtf bamfile.bam

Version: 1.5.1
Platform: Linux-x86_64

Link to one of the problem bam files:
https://www.dropbox.com/s/1bro5ohi4p...GCA-1.bam?dl=0

Any help would be highly appreciated

[hbrugge]

It would be really nice if anyone could look into this problem

[japrin]

I also encounter similar problem:

SAM_pairer_run: Assertion `1 != corrected_run'

But after I sort the bam file using PICARD, featureCounts worked fine.