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Old 10-04-2013, 02:41 AM   #1
tforde
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Default difficult executing bwa-mem

Hello all,
I am trying to run bwa mem. I have downloaded the program and exectued the 'make' command. However, when I try to run the bwa mem command, I get the message: [main] unrecognized command 'mem'

Any help you can provide on what further steps I need to take in order to be able to execute this command would be greatly appreciated.

Thanks!
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Old 10-04-2013, 03:09 AM   #2
harryzs
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please show us what you got after running 'make'
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Old 10-04-2013, 03:37 AM   #3
GenoMax
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Also post an example of the command line you are using to run bwa.
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Old 10-04-2013, 03:40 AM   #4
lh3
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Please use the latest version.
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Old 10-04-2013, 04:14 AM   #5
tforde
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Quote:
Originally Posted by harryzs View Post
please show us what you got after running '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 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 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
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Old 10-04-2013, 04:17 AM   #6
tforde
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Default Example of command line

Quote:
Originally Posted by GenoMax View Post
Also post an example of the command line you are using to run bwa.
bwa mem Erysipelothrix_genome.fasta MX1-H_uniq1.fastq MX1-H_uniq2.fastq > MX1-H.sam
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Old 10-04-2013, 04:18 AM   #7
tforde
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Default BWA version

Quote:
Originally Posted by lh3 View Post
Please use the latest version.
I'm using version 0.7.5a
Thanks for your help!
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Old 10-04-2013, 04:44 AM   #8
harryzs
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If I Just run
${path_to_bwa}/bwa

I get following message :
----------------------------------
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.5a-r405
Contact: Heng Li <lh3@sanger.ac.uk>

Usage: bwa <command> [options]

Command:
index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries

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
.....
----------------------------------

How about you??
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Old 10-04-2013, 04:53 AM   #9
tforde
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Quote:
Originally Posted by harryzs View Post
If I Just run
${path_to_bwa}/bwa

I get following message :
----------------------------------
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.5a-r405
Contact: Heng Li <lh3@sanger.ac.uk>

Usage: bwa <command> [options]

Command:
index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries

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
.....
----------------------------------

How about you??
This is what I am seeing:
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.6.1-r104
Contact: Heng Li <lh3@sanger.ac.uk>

Usage: bwa <command> [options]

Command: index index sequences in the FASTA format
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries
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
pac2cspac convert PAC to color-space PAC
stdsw standard SW/NW alignment

As you can see, mem does not appear to be in the list. I have already made all of the files in this directory executable. There are 5 bwamem files in this directory, which seems to be what other people have there as well.
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Old 10-04-2013, 05:11 AM   #10
winsettz
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Your version is
Quote:
Version: 0.6.1-r104
May want to redownload the latest from sourceforge?

http://sourceforge.net/projects/bio-bwa/files/

If you are feeling trusty, you can quickly pop this into your linux terminal

Code:
wget http://sourceforge.net/projects/bio-bwa/files/latest/download?source=files
And if multiple versions of bwa could be at play, type

Code:
which bwa
And see which version is being invoked when you type

Code:
bwa

Last edited by winsettz; 10-04-2013 at 05:54 AM.
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Old 10-04-2013, 05:48 AM   #11
GenoMax
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Quote:
Originally Posted by tforde View Post
I'm using version 0.7.5a
Thanks for your help!
It is possible that you have multiple versions of bwa installed on your machine (unless you are the "administrator" and know that there is only one version). In that case you are not using the newest version based on your other posts.
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Old 10-04-2013, 05:55 AM   #12
harryzs
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Just do what I did

run: ${path_to_bwa}/bwa

path_to_bwa = where you exectued the 'make' command
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Old 10-04-2013, 07:13 AM   #13
tforde
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Quote:
Originally Posted by winsettz View Post
Your version is

May want to redownload the latest from sourceforge?

http://sourceforge.net/projects/bio-bwa/files/

If you are feeling trusty, you can quickly pop this into your linux terminal

Code:
wget http://sourceforge.net/projects/bio-bwa/files/latest/download?source=files
And if multiple versions of bwa could be at play, type

Code:
which bwa
And see which version is being invoked when you type

Code:
bwa
It was indeed an issue with multiple versions downloaded; had to get some help here to redirect the path, but now appears to be working. Thanks very much for your help!
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