HTSeq count error while trying to read bam file

Question

[oozcan18]

Hello,

I would like to ask a question. While trying to get raw counts from bam file with htseq-count, it is throwing an error i that i couldn't find a solution. In short I'm reproducing some rna-seq data.

Here is my input:

htseq-count --format bam --order pos --mode intersection-strict --stranded reverse --minaqual 1 --type exon --idattr gene_id file.bam file.gtf  > file.tsv

and this is the error that i get:

29438 GFF lines processed.
Error occured when reading beginning of SAM/BAM file.
  _open() got an unexpected keyword argument 'check_sq'
  [Exception type: TypeError, raised in csamtools.pyx:476]

Thanks for your reply

[oozcan18]

This is the header of bam file, if anyone needs.

@HD VN:1.0  SO:coordinate
@SQ SN:1    LN:422616
@SQ SN:2    LN:457013
@SQ SN:3    LN:481791
@SQ SN:4    LN:513455
@SQ SN:5    LN:528682
@SQ SN:6    LN:536163
@SQ SN:7    LN:584452
@SQ SN:8    LN:739753
@SQ SN:9    LN:810151
@SQ SN:10   LN:839707
@SQ SN:11   LN:852849
@SQ SN:12   LN:859119
@SQ SN:13   LN:866983
@SQ SN:14   LN:852727
@SQ SN:15   LN:902900
@SQ SN:16   LN:908485
@SQ SN:17   LN:1232258
@SQ SN:18   LN:1253087
@SQ SN:19   LN:1282939
@SQ SN:20   LN:1621617
@SQ SN:Mito LN:32211
@SQ SN:Chloro   LN:149987
@RG ID:CM_Rep1  SM:CM   LB:CM_BL_N_Rep1 PL:ILLUMINA PU:CXX1234-ACTGAC.1
@PG ID:hisat2   PN:hisat2   VN:2.1.0    CL:"/home/engz46/Desktop/rna_seq/tuto/CM_RNA_SEQ/aligment/../../tools/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -p 8 --rg-id=CM_Rep1 --rg SM:CM --rg LB:CM_BL_N_Rep1 --rg PL:ILLUMINA --rg PU:CXX1234-ACTGAC.1 -x ../index/CM_fa_idx --dta --rna-strandness RF -S ../aligment/CM_BL_N_Rep1.sam -1 ../reads/SRR3726664_1.fastq -2 ../reads/SRR3726664_2.fastq"

[colin.kern]

That error is saying that a function is being called incorrectly. It's an error in the code, not in your input. This is probably being caused by incompatible versions of different python packages being installed. It can be pretty annoying to fix these kinds of issues, but reinstalling the software is always a good place to start.

[oozcan18]

Now, I solved the problem. For some reason, github version of htseq worked without causing a problem.

https://github.com/simon-anders/htseq

[oozcan18]

Thank you for your reply. It could solve my issue probably, but somehow, I managed to make it worse. But that is because of me probably.

Traceback (most recent call last):
  File "/home/engz46/anaconda2/bin/htseq-count", line 4, in <module>
    __import__('pkg_resources').run_script('HTSeq==0.11.2', 'htseq-count')
  File "/home/engz46/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/engz46/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1444, in run_script
    .format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/htseq-count' not found in metadata at '/home/engz46/.local/lib/python2.7/site-packages/HTSeq-0.11.2.dist-info'

Answer 1

[roisinkearins]

How did you fix this error? I currently have both of these appearing