Appears to be fixed now, see
I'll wait for a new release rather pull this from the development site.
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The man page bwa.1 has been updated for v 0.7.6 and it still has an 'aln' command. The c-code appears to still be there so this appears to be an oversight. I'm reverting th 0.7.5a rather than rewrite my workflows.
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It's not just you, it seems that that most recent version is missing aln (as well as samse and sampe). I don't see mention of this in either the NEWS file or the mailing list, but presumably this was done on purpose since the commands were removed from main.c (it looks like the source for them is there, you just can't get to them).
@GenoMax: I guess I hadn't read that quote to mean that they were actually removed, though I guess that that must be the reason.
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From Heng Li in the "NEWS" file of the new bwa release:
There are no changes to BWA-backtrack in this release. However, it has a few
known issues yet to be fixed. If you prefer BWA-track, It is still advised to
use bwa-0.6.x.
While I developed BWA-MEM, I also found a few issues with BWA-SW. It is now
possible to improve BWA-SW with the lessons learned from BWA-MEM. However, as
BWA-MEM is usually better, I will not improve BWA-SW until I find applications
where BWA-SW may excel.Last edited by GenoMax; 02-12-2014, 02:19 AM.
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bwa - unrecognized command 'aln'
Hi,
I try to run bwa with se reads, but it seems that bew can't find the aln option.
This is my bwa version:
Code:USER:~/software/bwa$ which bwa /usr/local/bin/bwa USER:bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.6a-r433 Contact: Heng Li <[email protected]> Usage: bwa <command> [options] Command: index index sequences in the FASTA format mem BWA-MEM algorithm fastmap identify super-maximal exact matches fa2pac convert FASTA to PAC format pac2bwt generate BWT from PAC pac2bwtgen alternative algorithm for generating BWT bwtupdate update .bwt to the new format bwt2sa generate SA from BWT and Occ Note: To use BWA, you need to first index the genome with `bwa index'. There are three alignment algorithms in BWA: `mem', `bwasw', and `aln/samse/sampe'. If you are not sure which to use, try `bwa mem' first. Please `man ./bwa.1' for the manual.
But in compiling bwa there was 'aln'
Code:USER:~/software/bwa-0.7.6a$ make gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o malloc_wrap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:878:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:952:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
Code:bwa aln genome/bwa/Bsub168.fasta NG6444_1_S_1.fastq > bwa_head_aln.sai
any ideas?
Assa
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