Error in htseq-count

[diego diaz]

Hi all,

I am having a problem when I try to run htseq-count. This is the sentence that I am using:

htseq-count -f bam -s no -i ID -t window mybam.bam genes.tab.gff3 > counts_file.count

This is the error:

77000 GFF lines processed.
Error occured when reading beginning of SAM/BAM file.
object of type 'NoneType' has no len()
[Exception type: TypeError, raised in _HTSeq.pyx:771]


And this is my bam header:

@HD VN:1.0
@SQ SN:chr1 LN:197195432 AS:mm9 SP:Mus musculus
@SQ SN:chr2 LN:181748087 AS:mm9 SP:Mus musculus
@SQ SN:chr3 LN:159599783 AS:mm9 SP:Mus musculus
@SQ SN:chr4 LN:155630120 AS:mm9 SP:Mus musculus
@SQ SN:chr5 LN:152537259 AS:mm9 SP:Mus musculus
@SQ SN:chr6 LN:149517037 AS:mm9 SP:Mus musculus
@SQ SN:chr7 LN:152524553 AS:mm9 SP:Mus musculus
@SQ SN:chr8 LN:131738871 AS:mm9 SP:Mus musculus
@SQ SN:chr9 LN:124076172 AS:mm9 SP:Mus musculus
@SQ SN:chr10 LN:129993255 AS:mm9 SP:Mus musculus
@SQ SN:chr11 LN:121843856 AS:mm9 SP:Mus musculus
@SQ SN:chr12 LN:121257530 AS:mm9 SP:Mus musculus
@SQ SN:chr13 LN:120284312 AS:mm9 SP:Mus musculus
@SQ SN:chr14 LN:125194864 AS:mm9 SP:Mus musculus
@SQ SN:chr15 LN:103494974 AS:mm9 SP:Mus musculus
@SQ SN:chr16 LN:98319150 AS:mm9 SP:Mus musculus
@SQ SN:chr17 LN:95272651 AS:mm9 SP:Mus musculus
@SQ SN:chr18 LN:90772031 AS:mm9 SP:Mus musculus
@SQ SN:chr19 LN:61342430 AS:mm9 SP:Mus musculus
@SQ SN:chrM LN:16299 AS:mm9 SP:Mus musculus
@SQ SN:chrX LN:166650296 AS:mm9 SP:Mus musculus
@SQ SN:chrY LN:15902555 AS:mm9 SP:Mus musculus
@RG ID:CNhs13087.11810-124E1.nobarcode SM:11810-124E1 LB:CNhs13087 PU:Heliscope CN:GeNAS DT:2011-05-06 00:00:00 PL:OP-HELISCOPE-CAGE-v4.0
@PG IDelve VNelve 0.9 CL:/quality_control/development/bin/delve -u 1 -o /tmp/964608.1.all.q/tE0acLw1vu.sam -m /tmp/964608.1.all.q/TaiL4zcI8M/model/CNhs13087.model -t 8 align /tmp/964608.1.all.q/TaiL4zcI8M/temp/CNhs13087_data/delve_seed/output/CNhs13087.2011_05_06_R2_30Q_1100FOV.fc2.ch15.11810-124E1.nobarcode.sam /tmp/964608.1.all.q/TaiL4zcI8M/temp/CNhs13087_data/genome_sequence/output/mm9_undefined_sex_type.fa
VHE-211910141003-15-998-2-3681 0 chr1 3000762 1 12M1I12M * 0 0 TGTTTTTTCTGTATTCCGTTTTAGT * NM:i:3MD:Z:16T3C3 XP:Z:H<@@~~~~=>=1!-./*(*******
VHE-211910141003-15-46-2-844 528 chr1 3000859 3 7M1I18M1I4M1I8M1I9M * 0 0 CGGAGCCGCTCTGCTAGCTGTTAGCTGTAGCTATGCGGTCTCCGTGCCGG * NM:i:14 MD:Z:0T2G1G5A14G4T0T3A2A3G2 XP:Z:&%%#%$$!$%%&&&&&&''''''''&!%%&&!&&~~~~~%#~6797++7O
VHE-211910141003-15-1032-0-2496 0 chr1 3001837 7 2M2D19M * 0 0 CTAGCTGACTCTCTAGACAGC * NM:i:2 MD:Z:2^TG19 XP:Z'))---~~~~=>>~~~~L@F


I don't know what is wrong. Please can you give me some advice?

Thanks in advance!

[reema]

Hello diego,

Here the solution http://sourceforge.net/p/htseq/bugs/12/

[diego diaz]

Thanks reema

[jay2utee]

Thanks, all, for the pointers, but I'm still unclear as to how to apply the solution that's mentioned in the bug report (which is still tagged as "open").

I found the three instances of the string that needed correction (per the advice in the report), changed them and recompiled, but I still get the same error.

-John

[dpryan]

You might just give featureCounts a try. It should be faster anyway.