SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
some error message from BFAST match lei Bioinformatics 6 11-23-2015 04:42 AM
Error during Bfast match step James W. MacDonald Bioinformatics 2 01-05-2011 07:15 AM
BFAST match/localalign help Esther Bioinformatics 3 08-04-2010 06:19 AM
BFAST match problem blu78 Bioinformatics 20 08-03-2010 02:27 AM
bfast match segmentation fault jmartin Bioinformatics 6 04-14-2010 01:21 AM

Reply
 
Thread Tools
Old 02-07-2011, 09:55 AM   #1
sammy07
Member
 
Location: austria

Join Date: Nov 2010
Posts: 20
Default bfast match problem on fedora 14

Hi everybody,

I cant make bfast work on Fedora 14.
I'm using unpaired SOLID data of 50 bp length.
In version 0.6.4e, the solid2fastq step did not work properly for me. In the last version (0.6.4f git:50fb580ff23fe839b72b49924908159bd35d6f86) from the git repository, the bfast match step fails with the following error message:

...
In total read 1 contigs for a total of 3171952 bases
************************************************************
Reading /home/user/work/analysis/reads.1.fastq into a temp file.
bfast: ../bfast/RGMatch.c:155: RGMatchPrint: Assertion `m->readLength > 0' failed.

The performed steps were:
1) solid2fastq -n 10000000 -o reads datafile.csfasta datafile.qual
2) ~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna
~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna -A 1
3) bfast index -f refGenome.fna -m 11111... -w 14 -i 1 -A 1 -n 8
4) bfast match -f refGenome.fna -A 1 -r reads1.fastq -n 8 > tmp.bmf

I want to try it on a virtual machine running Fedora 13. Would be happy about any further suggestions... Thanks in advance!
sammy07 is offline   Reply With Quote
Old 02-07-2011, 10:01 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Looks like a read with zero bases, could you check for that in your fastq file?

Quote:
Originally Posted by sammy07 View Post
Hi everybody,

I cant make bfast work on Fedora 14.
I'm using unpaired SOLID data of 50 bp length.
In version 0.6.4e, the solid2fastq step did not work properly for me. In the last version (0.6.4f git:50fb580ff23fe839b72b49924908159bd35d6f86) from the git repository, the bfast match step fails with the following error message:

...
In total read 1 contigs for a total of 3171952 bases
************************************************************
Reading /home/user/work/analysis/reads.1.fastq into a temp file.
bfast: ../bfast/RGMatch.c:155: RGMatchPrint: Assertion `m->readLength > 0' failed.

The performed steps were:
1) solid2fastq -n 10000000 -o reads datafile.csfasta datafile.qual
2) ~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna
~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna -A 1
3) bfast index -f refGenome.fna -m 11111... -w 14 -i 1 -A 1 -n 8
4) bfast match -f refGenome.fna -A 1 -r reads1.fastq -n 8 > tmp.bmf

I want to try it on a virtual machine running Fedora 13. Would be happy about any further suggestions... Thanks in advance!
nilshomer is offline   Reply With Quote
Old 02-07-2011, 11:30 AM   #3
sammy07
Member
 
Location: austria

Join Date: Nov 2010
Posts: 20
Default

Hi Nils,

you are right, this seems to be a problem with the data integrity. The problem looked like that:

@160_774_71
T022221123122231102
+
BBBBBBABBABBABBBBABB+'))?@;55<<6@/);/1<5?91)-/5@9+

If these four lines are removed from the file, it works. Thank you!
sammy07 is offline   Reply With Quote
Old 02-07-2011, 12:14 PM   #4
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

If you run the "solid2fastq" step again, do you get the same problem read? Could you pull out the same read in the CSFAST/QUAL files so I can see what is going on?
nilshomer is offline   Reply With Quote
Old 02-08-2011, 08:40 AM   #5
sammy07
Member
 
Location: austria

Join Date: Nov 2010
Posts: 20
Default

Ok, it seems that one pair of my .csfasta / .qual files was broken. Both just stop in the middle of a line without a newline character, which produces the short read in the solid2fastq output.

Another strange thing is that the .csfasta and the corresponding .qual file even have a different number of entries (the .qual file is longer), and solid2fastq did not produce any error message concerning this; possibly it just discarded the rest.
sammy07 is offline   Reply With Quote
Old 02-08-2011, 09:24 AM   #6
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Sounds like your .csfasta / .qual files are corrupt. They should (IRC) have the same # of lines. It might be a good time to call up some support,

Nils
nilshomer 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 09:20 PM.


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