Error in HTSEQ

[komalsrathi]

Hi everyone,

I am using the latest version of GSNAP to get alignments for 29 RNAseq samples. So after I get a SAM alignment from GSNAP, I use samtools to convert it into BAM and then:

samtools fixmate input.bam input_unsortfix.bam

samtools view -f 0x0002 input_unsortfix.bam | htseq-count -s reverse - Homo_sapiens.GRCh37.73.protein_linc.gtf > input.counts

My GTF file contains only protein coding & lincRNAs and it is the latest version. I get the following error after running htseq-count command:

Error: 'itertools.chain' object has no attribute 'get_line_number_string'[Exception type: AttributeError, raised in count.py:201]

I have successfully run around 15 samples but I am getting this error in the other 14 samples. How can I solve this issue?

[Simon Anders]

Are you using the newest version? I've fixed the 'get_line_number_string' issue two weeks ago.

[komalsrathi]

Hi Simon,

I am using "Part of the 'HTSeq' framework, version 0.5.4p1". I will update it to the latest version. Thanks for the prompt reply.

[komalsrathi]

Are you using the newest version? I've fixed the 'get_line_number_string' issue two weeks ago.

Hi Simon,

I updated htseq-count to version 0.5.4p5 and now I am getting a different error but for the same file:

Error occured when processing SAM input (line 50956571):
("Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared", 'line 50956571')
[Exception type: ValueError, raised in _HTSeq.pyx:1323]

This is line no. 50956571. As you can see it contains only Ns.

HWI-ST1006:111:D2AADACXX:3:2208:1098:73812	165	*	0	0	*	chr20	44474350	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	###################################################################################################	RG:Z:C00079

[komalsrathi]

The issue is solved. I parsed my alignments to remove any alignment matching '\t\*\t' pattern. Thanks