SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
htseq-count paolo.kunder Bioinformatics 10 10-22-2014 04:45 AM
htseq-count low count problem gandalf886 Bioinformatics 3 08-23-2014 07:05 AM
HTseq-count of zero halffedelf RNA Sequencing 14 04-17-2014 10:31 AM
multiBamCov or htseq-count to count read per feature ? NicoBxl Bioinformatics 1 07-03-2012 02:05 AM
HTSeq errors wangli RNA Sequencing 4 06-09-2012 02:55 PM

Reply
 
Thread Tools
Old 05-07-2015, 03:43 PM   #1
virg4l
Junior Member
 
Location: Midwest

Join Date: May 2015
Posts: 7
Default HTseq-count errors

I put 10 .bam files (from Tophat) through the same samtools & htseq-count commands, and 3/10 didn't work (each with their own error) in htseq.

$ samtools view -h -o sample.sam sample.bam

$ htseq-count --stranded no -i gene_id sample.sam genes.gtf > sample.gene.counts

The errors are:

1) ...596437 GFF lines processed.
Error occured when reading beginning of SAM/BAM file.
[Exception type: StopIteration, raised in count.py:84]

This one particularly confuses me since the program didn't choke on any of the other sam files that were prepared the same way.

2) ...20000000 SAM alignment records processed.
Error occured when processing SAM input (line 20080682 of file TH2/DEprep/BR2_N2In.sam):
('SAM line does not contain at least 11 tab-delimited fields.', 'line 20080682 of file TH2/DEprep/BR2_N2In.sam')
[Exception type: ValueError, raised in _HTSeq.pyx:1276]

3) ...35089676 SAM alignments processed.
[Errno 5] Input/output error
[Exception type: IOError, raised in count.py:212]


Any suggestions for how I should fix these problems?
virg4l is offline   Reply With Quote
Old 05-07-2015, 11:20 PM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

I wonder if you're having hard drive corruption issues.

In any case, make sure you're using the most recent version of htseq-count. Also, check line 20080682 of the sam file mentioned and ensure it's not malformed.
dpryan is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:50 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO