SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools faidx Segmentation fault baohua100 Bioinformatics 19 04-19-2016 08:09 AM
weird samtools tview errors iwtwb8 Bioinformatics 2 04-29-2011 02:54 PM
purpose of faidx and bai bioxyz Bioinformatics 6 09-08-2010 09:14 AM
tophat errors Greg Bioinformatics 0 01-12-2010 09:55 AM
Tophat errors alig Bioinformatics 3 08-17-2009 08:37 AM

Reply
 
Thread Tools
Old 07-12-2011, 10:36 PM   #1
ashwatha
Member
 
Location: India

Join Date: Jul 2011
Posts: 14
Question Samtools faidx errors

Hi,

I am new to samtools and bioinformatics in general. I have a quick question about generating a fasta index file from a .fa file. I see a segmentation fault while running samtools faidx on hg19:

$samtools faidx hg19.fa
[fai_build_core] different line length in sequence 'chr1'.
Segmentation fault

This is probably a dumb question, but what could be causing this?

Thanks!
ashwatha is offline   Reply With Quote
Old 07-13-2011, 05:32 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

You have differing line lengths after chromosome one. Check that each line in chr1 has the same length (except for the last, which should be equal to or shorter).
nilshomer is offline   Reply With Quote
Old 07-13-2011, 07:23 PM   #3
ashwatha
Member
 
Location: India

Join Date: Jul 2011
Posts: 14
Default

Thanks - I didn't know that every line had to be the same length.
ashwatha is offline   Reply With Quote
Old 09-08-2015, 08:06 AM   #4
annrose
Junior Member
 
Location: netherlands

Join Date: Jun 2014
Posts: 4
Default

samtools faidx hg19.fa
[fai_build_core] different line length in sequence 'chrY'

hi i have the same problem.....can you tell how can i correct the length?? i am very new to these stuff
annrose is offline   Reply With Quote
Reply

Tags
fasta, fasta index, samtools

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 11:22 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO