Comments (4)
mluypaert
commented on September 24, 2024
@val-antonescu @gbottu @BenLangmead
This is still an issue (in the current Bowtie 1.1.2). For more details, see the latest comments on this sourgeforge ticket.
Can anyone please fix this for good?
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ch4rr0
commented on September 24, 2024
@mluypaert -- I am working on a fix for this (will reply with ETA). In the meantime if you intend on running bowtie with a large index can you please include the --large-index option. That should resolve the issue in the interim.
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mluypaert
commented on September 24, 2024
@ch4rr0
Thanks for the tip (I was aware of it). Before publishing a new release (after fixing this issue), please ensure that #35 (an issue I just created) gets fixed as well. To my opinion, issue #35 is even more urgent than this issue, as there is no easy fix for it (as far as I know) and it probably happens unnoticed with many other users (since bowtie does not report any errors).
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ch4rr0
commented on September 24, 2024
A fix for this issue was included as part of our most recent release.
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Related Issues (20)
- bowtie 1.3.0 generated sam files error HOT 11
- Migrate Travis CI by May 31, 2021
- bowtie install error on Apple M1 HOT 1
- Mismatch flag
- Bowtie hangs when running on very large genomes HOT 8
- -M option reports the wrong number of reads processed HOT 2
- problem with option -n and -l
- XM:i SAM Optional field ... seems like hits + 1 for all hits? HOT 3
- Bowtie no longer works with updated versions of tbb
- Error: reads file does not look like a FASTQ file HOT 2
- Bowtie not mapping 100% HOT 1
- -m setting not outputting a sam file with an -NH tag
- Questions about tracking the history of building index
- Some reference entries show up as duplicates HOT 1
- Cline paired 2 (fw:1, sam:1) test aborted with -Wp,-D_GLIBCXX_ASSERTIONS HOT 4
- Is there an equivalent of "Bowtie2 --very-sensitive" for Bowtie1 [suggested label = Question]
- Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2 HOT 1
- secondary alignment flag
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