[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.

[hbrugge]

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

[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/1bro5ohi4pyck8c/cell_1602_CAATTCTGCTAGCA-1.bam?dl=0

Any help would be highly appreciated

[shi]

Can you update to Subread 1.5.1 and try again?

[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

[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?

[shi]

What is the version of featureCounts you use?

[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]

That's great. Thanks for letting us know.

[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.

[santhilalsubhash]

Thanks a lot. I will wait for that.

[shi]

We have downloaded the bam file and found that the problem was caused by excessively long bam header lines.

We will try to fix this and release a patched version soon.

[santhilalsubhash]

samtools view 0ab4dac4-bbb9-4cd5-ae67-9469c6e8f21b/G28064.MDA-MB-468.1.bam | head

C1E2NACXX130117:1:1309:3032:16444	419	1	11199	3	101M	=	11938	840	CCGCTTGCTCACGGTGCTGTGCCAGGGCGCCCCCTGCTGGCGACTAGGGCAACTGCAGGGCTCTCTTGCTTAGAGTGGTGGCCAGCGCCCCCTGCTGGGGC	CCCFFFFFHGHHHJEHJIIHIJJEJJJDHIJJJ<DFGGHIGIGGGFFCBCABBCCACCDDDDDDDDCDCDDCDC###########################	CC:Z:15	PG:Z:MarkDuplicates.3A	RG:Z:C1E2N.1	NH:i:2	HI:i:0	NM:i:1	CP:i:102519871	MQ:i:3	UQ:i:2
C1E2NACXX130117:1:1309:3032:16444	339	1	11938	3	101M	=	11199	-840	AGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTG	344<5@<>@??A@BDCC?;93BCD=BBE=EEDHIGEGEA@;>CEFB<HGD@HDIIIGIIJJJIIJIJIJJJJJIFGIJIHIJIJJJJIHHHGHFFFFFCCC	CC:Z:15	PG:Z:MarkDuplicates.3A	RG:Z:C1E2N.1	NH:i:2	HI:i:0	NM:i:0	CP:i:102519132	MQ:i:3	UQ:i:0
C1E2NACXX130117:2:1305:12347:47337	355	1	12040	0	101M	=	12113	174	GCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTCCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTG	CC@FFFFDHHHHGIJJDGCEHIIICEEFGEHGIIGGGGGGGGIHIGIIIGHJJJIJIGIHGEEGHFHHFFDEDCECEDDDDEDDEDDDDDDD?BCCCCCDA	CC:Z:15	PG:Z:MarkDuplicates.2C	RG:Z:C1E2N.2	NH:i:5	HI:i:0	NM:i:1	CP:i:102519030	MQ:i:0	UQ:i:38
C1DVPACXX130111:2:2210:2530:60149	163	1	12042	0	101M	=	12082	141	CAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCA	CCCFFDDFHHHHHIIJJJJJJJGIFGIIJIJJJJJJJHIJIJIJJJJJJJEHIJJIJIJFHIJJJHHHFFFFFDEDEEEEDDEDCCDDDDBDDDDCDDDD#	CC:Z:15	PG:Z:MarkDuplicates.2R	RG:Z:C1DVP.2	NH:i:5	HI:i:0	NM:i:0	CP:i:102519028	MQ:i:0	UQ:i:0
D1JYHACXX130117:5:2113:9637:43505	345	1	12048	0	101M	=	12048	0	GCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAAC	<<DCC?:>DC@;ACCCA<CCCCACA@@A>?D@CBHGEHHGDIJJIIHIJJJJJIJJJJJJIFHHJJJJIJIIIJIIJIJJJJJJJIJIHFHHHFFFFFC@C	CC:Z:15	PG:Z:MarkDuplicates.33	RG:Z:D1JYH.5	NH:i:6	HI:i:0	NM:i:0	CP:i:102519022	UQ:i:0
C1E2NACXX130117:6:1102:7112:41762	165	1	12055	0	*	=	12055	0	CGCGCCTCCGCCGGCGCGCCGCGCCTCTCCGCACCTCTCCGCGCCTCCGCCGGCGCGCCGCCTTTGCGAGGGCGGAGTTGCGTTCTCTTTAGCACACAGCC	@@@DDDDDHFFFHAHGDD>GFG=A9B<@CCBBBBBC?>CC837@B8-?@BBB&07@B57B@B@;CCA7>99;;;95<+9+:-5<BBA>CC3>>CAA?@?AA	PG:Z:MarkDuplicates.30	RG:Z:C1E2N.6
C1E2NACXX130117:6:1102:7112:41762	89	1	12055	0	101M	=	12055	0	GAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATAC	###########@CCCAAA?;=2@@66(3;@FFE?HFGIGIIIHFF@DEHGGGHDF>GDBBB:GHFBCIGHFC::;@EIIIIGCFIEBHFA?BBDDFDD<??	CC:Z:15	PG:Z:MarkDuplicates.30	RG:Z:C1E2N.6	NH:i:6	HI:i:0	NM:i:0	CP:i:102519015	UQ:i:0
C1DVPACXX130111:2:2210:2530:60149	83	1	12082	0	101M	=	12042	-141	AGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGG	3CDDDDDDDDDDDDDDDDDDDEEECCFEDDFHFGHHJIJJJJJJJIGJIJJJIJJIJJJJJJJJJIJJIJJIHJIHJIGJJJIJJJIJHHHHHFFFFFCCC	CC:Z:15	PG:Z:MarkDuplicates.2R	RG:Z:C1DVP.2	NH:i:5	HI:i:0	NM:i:0	CP:i:102518988	MQ:i:0	UQ:i:0
C1E2NACXX130117:2:1305:12347:47337	403	1	12113	0	101M	=	12040	-174	TTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCGTCAACTTCTCT	?DDDCDCDDDDDBDDDB?CDFFFFHGGHHHJJIJJJIJIGF=IIJIHDHGGIIIJIIIIIJJJJIJJIJJIJJJJIJJJJIJIJJJIHF<HFHFFFFFCCC	CC:Z:15	PG:Z:MarkDuplicates.2C	RG:Z:C1E2N.2	NH:i:5	HI:i:0	NM:i:1	CP:i:102518957	MQ:i:0	UQ:i:27
C1E2NACXX130117:7:1102:9623:27660	355	1	12294	1	101M	=	12318	125	CCCCTACCTGCCGTCTGCTGCCATCGGAGCCCAAAGCCGGGCTGTGACTGCTCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAGGTCTGGCTTTGGCCCT	CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFEDDDDDDDDDDDDDDDDDDDDDDDCBD?CDDDDDDDDDDDB?	CC:Z:15	PG:Z:MarkDuplicates.2A	RG:Z:C1E2N.7	NH:i:3	HI:i:0	NM:i:0	CP:i:102518776	MQ:i:1	UQ:i:0

Link to screeshot:

[shi]

OK, could you please just post the first few reads before we try to download the data?

[santhilalsubhash]

Hello Wei Shi,

Thanks for your reply. But the problem is these BAM files are not publicly accessible. But if you have access to CGHub you can try downloading BAM file with this analysis id "0ab4dac4-bbb9-4cd5-ae67-9469c6e8f21b" using GeneTorrent. More info on this BAM file