Question: failed to transcriptom indexing with tophat2
0
gravatar for F
3.7 years ago by
F3.4k
Iran
F3.4k wrote:

sorry guys,

please some one help me to know why i face with error whenever im trying this syntax???

[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat2 -G yeast_SGD_anno.gtf --transcriptome-index=transcriptome Saccharomyces_cerevisiae.R64-1-1.pep.all.bt2idx

[2015-09-03 14:36:44] Building transcriptome files with TopHat v2.1.0
-----------------------------------------------
[2015-09-03 14:36:44] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-09-03 14:36:44] Checking for Bowtie index files (genome)..
[2015-09-03 14:36:44] Checking for reference FASTA file
[2015-09-03 14:36:44] Building transcriptome data files transcriptome/yeast_SGD_anno
[2015-09-03 14:36:44] Building Bowtie index from yeast_SGD_anno.fa
    [FAILED]
Error: Couldn't build bowtie index with err = 1
[izadi@lbox161 bowtie2-2.2.5]$ 

myposts tophat2 bowtie2 • 1.5k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 3.7 years ago by F3.4k
1

You'll have to go through the logs, manually execute the last command that tophat2 issued, and look at the error message that that gives.

ADD REPLYlink written 3.7 years ago by Devon Ryan90k

thanks Devon,

in logs:

[2015-09-03 10:56:10] Building transcriptome files with TopHat v2.1.0
-----------------------------------------------
[2015-09-03 10:56:10] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

and

 ./tophat -G yeast_SGD_anno.gtf --transcriptome-index=transcriptome orf_coding.fasta

 

 

ADD REPLYlink written 3.7 years ago by F3.4k

Wrong log, there's one that lists the exact commands being run.

ADD REPLYlink written 3.7 years ago by Devon Ryan90k

sorry there are:

bowtie_inspect_recons.log in which:

bowtie-inspect: bt2_inspect.cpp:234: void print_ref_sequences(std::ostream&, bool, const EList<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, 128>&, const TIndexOffU*, const std::string&): Assertion `0' failed.

tophat.log in which:

[2015-09-03 14:36:44] Building transcriptome files with TopHat v2.1.0
-----------------------------------------------
[2015-09-03 14:36:44] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-09-03 14:36:44] Checking for Bowtie index files (genome)..
[2015-09-03 14:36:44] Checking for reference FASTA file
[2015-09-03 14:36:44] Building transcriptome data files transcriptome/yeast_SGD_anno
[2015-09-03 14:36:44] Building Bowtie index from yeast_SGD_anno.fa
    [FAILED]
Error: Couldn't build bowtie index with err = 1

run.log in which:

/usr/data/nfs6/izadi/test/tophat-2.1.0.Linux_x86_64/tophat -G yeast_SGD_anno.gtf --transcriptome-index=transcriptome Saccharomyces_cerevisiae.R64-1-1.pep.all.bt2idx
/usr/data/nfs6/izadi/test/tophat-2.1.0.Linux_x86_64/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip --gtf-annotations transcriptome/yeast_SGD_anno.gff --no-closure-search --no-coverage-search --no-microexon-search transcriptome/yeast_SGD_anno.gff Saccharomyces_cerevisiae.R64-1-1.pep.all.bt2idx.fa transcriptome/yeast_SGD_anno.fa > ./tophat_out/logs/g2f.out
./bowtie2-build transcriptome/yeast_SGD_anno.fa transcriptome/yeast_SGD_anno

and the file named g2f.err that i could not open 

 

 

 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by F3.4k
1

If transcriptome/yeast_SGD_anno.fa still exists, then have a look at it. Presumably it has some sort of issue.

ADD REPLYlink written 3.7 years ago by Devon Ryan90k

yeah Devon it is in transcriptome file in bowtie2 folder but i could not open that

ADD REPLYlink written 3.7 years ago by F3.4k
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