Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
bowtie2-inspect mdb@wistar Bioinformatics 2 02-04-2013 10:50 AM
bowtie2 chomp error frej.tulin Illumina/Solexa 2 01-29-2013 11:26 AM
assembly error in bowtie2 shin_enomoto Bioinformatics 0 07-11-2012 09:42 AM
Bow-tie inspect returned an error pettervikman Bioinformatics 8 07-13-2011 12:41 AM
PubMed: Great expectations: using massively parallel sequencing to solve inherited di Newsbot! Literature Watch 0 10-23-2010 02:01 AM

Thread Tools
Old 02-15-2013, 04:50 AM   #1
Location: Germany

Join Date: Nov 2012
Posts: 22
Default need help to solve bowtie2-inspect error

Dear all bowtie users,

I am new in NG-sequencing. I used following command to build index of repeat masked genome by repeatmasker.

bowtie2-build genome_scaffolds.masked.fa my_genome_index

during the execution of command I also faced the multiple warnings
'Warning: Encountered reference sequence with only gaps'

Furthermore, during using Tophat I got warning: could not find fasta file and error Error: bowtie-inspect returned an error log: bowtie2-inspect: bt2_inspect.cpp:218:

So, after reading some blogs I thought to build fasta from index and used

bowtie2-inspect my_genome_index

assert_eq: expected (24026, 0x5dda) got (23330, 0x5b22)
bowtie2-inspect: bt2_inspect.cpp:218: void print_ref_sequences(std:stream&, bool, const EList<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, 128>&, const uint32_t*, const std::string&): Assertion `0' failed.

The command again failed with the above message. Could someone please help me to solve this problem

below is the footer first bowtie execution
len: 192701494
bwtLen: 192701495
sz: 48175374
bwtSz: 48175374
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 12043844
offsSz: 48175376
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 1003654
numLines: 1003654
ebwtTotLen: 64233856
ebwtTotSz: 64233856
color: 0
reverse: 1

Thank you for your HELP!
Shishir is offline   Reply With Quote
Old 07-18-2013, 09:31 AM   #2
Location: china

Join Date: Mar 2011
Posts: 31

Did you fingure out what is the problem?
11xinqi is offline   Reply With Quote

bioinfomatics, bowti2-output, bowtie index, rnaseq, tophat

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 02:16 AM.

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