SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
sam to bam conversion error, no @SQ lines in the header, missing header? efoss Bioinformatics 17 12-03-2015 04:28 AM
BWA sam and Samtools sam->bam conversion problem maasha Bioinformatics 6 06-05-2013 07:39 AM
samtools: parse error in SAM to BAM conversion chrisW Bioinformatics 12 01-14-2013 06:16 PM
Bowtie2 Sam output Derek-C Bioinformatics 3 11-13-2012 11:10 AM
Tophat v1.1.4 potential error with sam to bam conversion? jb2 Bioinformatics 6 11-17-2011 12:52 AM

Reply
 
Thread Tools
Old 11-16-2012, 10:39 PM   #1
a_mt
Member
 
Location: C:/Program files/Google/Chrome

Join Date: Jul 2012
Posts: 34
Post bowtie2 output, sam to bam conversion error.

Hi all,

I am trying convert a sam file (PE bowtie2 default fr output) to bam file using samtools view command. But it's throwing the following error.

Code:
$ samtools view -bS -o aln3.bam aln3.sam
[samopen] SAM header is present: 17 sequences
[sam_read1] reference '451450' is recognized as '*'
Parse error at line 2026299: sequence and quality are inconsistent
When I looked at the partcular line,
Code:
sed -n 2026299p aln3.sam
        133     chr12   451450  0       *       =       451450  0       *       *       YT:Z:UP YF:Z:LN
Its missing col1 (Qname) also CIGAR string, segment sequence and Quality scores are unavailable.

When I checked for such lines
Code:
$ sed -n '/^[^H]/=' aln3.sam | wc -l
5422
There were 5422 lines.

How do I proceed now?? Do I delete these 5422 lines from sam file?? This thread here had the same problem but it was with bwa aligner.


Also my bowtie output after aligning says (many such lines are produced before showing final alignment stats):

Code:
Warning: skipping mate #2 of read '' because length (0) <= # seed mismatches (0)
Warning: skipping mate #2 of read '' because it was < 2 characters long
I am not able interprte this. Also my alignement stats says 99.97% pairs were aligned concordantly 0 times. I am bit amused.
Code:
1018542 reads; of these:
  1018542 (100.00%) were paired; of these:
    1018249 (99.97%) aligned concordantly 0 times
    188 (0.02%) aligned concordantly exactly 1 time
    105 (0.01%) aligned concordantly >1 times
How do I proceed now??

Thank you.

Between I am new to analysis and I hope you people dont mind if my questions are too simple.

Last edited by a_mt; 11-16-2012 at 10:41 PM.
a_mt is offline   Reply With Quote
Old 03-21-2014, 01:27 PM   #2
arcolombo698
Senior Member
 
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default Skipping Mate errors

Hello. I have the same issue

Warning: skipping mate #1 of read 'SN860:381:H80WNADXX:1:1101:18171:2118 1:N:0:1' because length (0) <= # seed mismatches (0)
Warning: skipping mate #1 of read 'SN860:381:H80WNADXX:1:1101:18171:2118 1:N:0:1' because it was < 2 characters long
arcolombo698 is offline   Reply With Quote
Old 03-21-2014, 02:59 PM   #3
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

It sounds like you have a 0bp read, possibly due to quality trimming. You can try removing such reads (and their mates) with a tool that allows you to specify a minimum read length.
Brian Bushnell is offline   Reply With Quote
Old 03-29-2015, 01:23 AM   #4
gerbarinov
Junior Member
 
Location: RUSSIA MOSCOW

Join Date: Mar 2015
Posts: 3
Default

I solved this problem after trimming fastaq files with fastx_trimmer -f and fastx_trimmer -t operations with no 0bp read in output files. So the solution for me was to remove artifacts with fastx_artifacts_filter and then synchronize pairs with fastqCombinePairedEnd.py
gerbarinov 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 03:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO