New version of BWA fail at this step : 'bwa samp index.fa aln_1.sai aln_2.sai file_1.fastq file_2.fastq > aln.sam'
Error send -> "bwa_refine_gapped_core: Assertion `re - rb == rlen' failed."
All previous steps (bwa index and bwa aln) work great !
Same problem on MAC OsX.
Only older version (<=6.2) of bwa seems to be able to do the job with mine data...
ProblemType: Crash
DistroRelease: Ubuntu 13.10
Package: bwa 0.7.5a-2
ProcVersionSignature: Ubuntu 3.10.0-5.17-lowlatency 3.10.2
Uname: Linux 3.10.0-5-lowlatency x86_64
ApportVersion: 2.12-0ubuntu3
Architecture: amd64
AssertionMessage: bwa: bwase.c:182: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed.
CrashCounter: 1
Date: Mon Aug 12 18:43:24 2013
Dependencies:
gcc-4.8-base 4.8.1-8ubuntu1
libc6 2.17-91ubuntu1
libgcc1 1:4.8.1-8ubuntu1
multiarch-support 2.17-91ubuntu1
zlib1g 1:1.2.8.dfsg-1ubuntu1
EcryptfsInUse: Yes
ExecutablePath: /usr/bin/bwa
InstallationDate: Installed on 2013-08-07 (5 days ago)
InstallationMedia: Ubuntu-Studio 13.10 "Saucy Salamander" - Alpha amd64 (20130806)
MarkForUpload: True
ProcCmdline: bwa sampe HcpDNAm.fa R13_1.sai R13_2.sai R13_1.fastq.gz R13_2.fastq.gz
Signal: 6
SourcePackage: bwa
StacktraceTop:
__assert_fail_base (fmt=0x7f3598e883b8 "%s%s%s:%u: %s%sAssertion `%s' failed.\n%n", assertion=assertion@entry=0x435fd4 "re - rb == rlen", file=file@entry=0x435fc0 "bwase.c", line=line@entry=182, function=function@entry=0x4362c0 "bwa_refine_gapped_core") at assert.c:92
__GI___assert_fail (assertion=0x435fd4 "re - rb == rlen", file=0x435fc0 "bwase.c", line=182, function=0x4362c0 "bwa_refine_gapped_core") at assert.c:101
?? ()
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Title: bwa assert failure: bwa: bwase.c:182: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed.
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm audio cdrom dip lpadmin plugdev sambashare sudo
