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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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bowtie2-build only generate .3.bt2 and .4.bt2 two files #471

Open cyundi opened 2 months ago

cyundi commented 2 months ago

Hi everyone, I met a problem when using bowtie2 build to generate index for my reference database that it only generate .3.bt2 and .4.bt2 two files instead of six files, and there was no error:

Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 2558513 for bucket 1 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2558514 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 655618 fchr[G]: 1275466 fchr[T]: 1909757 fchr[$]: 2558513 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5056533 bytes to primary EBWT file: custom_ref_genomes/43404_1#100_bin.12.orig.fa.rev.1.bt2 Wrote 10234060 bytes to secondary EBWT file: custom_ref_genomes/43404_1#100_bin.12.orig.fa.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2558513 bwtLen: 2558514 sz: 639629 bwtSz: 639629 lineRate: 6 offRate: 0 offMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2558514 offsSz: 10234056 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13326 numLines: 13326 ebwtTotLen: 852864 ebwtTotSz: 852864 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:01

My command is: bowtie2-build custom_ref_genomes/*fa ref_index -offrate 4

Can anyone tell me how to fix it? Thanks!

ch4rr0 commented 2 months ago

Hello,

We pushed a change to the bug_fixes branch that changes the behavior of bowtie2-build to throw an exception if it encountered any issues while persisting the BWT. Would you be willing to test out the change?

Thank you