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Old 11-10-2010, 06:50 PM   #1
seq-nerd
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Default bwa index error

Hi, I'm having trouble indexing my genome. Here is the command I am using:

bwa index -a bwtsw /data/Bioinfo/genomes/hg18.fa

Here is the error:

[bwa_index] Pack FASTA... [bns_fasta2bntseq] fail to open file '/data/Bioinfo/genomes/hg18.fa.pac'. Abort!
Aborted

I have all the various hg18.fa files in the same directory as well:

hg18.fa
hg18.pac
hg18.ann
hg18.amb
hg18.rpac
hg18.bwt
hg18.rbwt
hg18.sa
hg18.rsa

I don't know what I'm doing wrong. Any suggestions would be appreciated! Thanks!
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Old 11-11-2010, 04:49 AM   #2
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try /data/Bioinfo/genomes/hg18.fa instead of /data/Bioinfo/genomes/hg18.fa.pac
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Old 11-11-2010, 04:55 AM   #3
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the various files are missing .fa in their extension.
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Old 11-11-2010, 04:55 AM   #4
seq-nerd
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I do not specify the .pac at the end. I don't know why the command is showing that. I specify only hg18.fa....any ideas?
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Old 11-11-2010, 04:59 AM   #5
seq-nerd
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the .fa's are i just forgot to type them.....
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Old 11-26-2010, 02:53 PM   #6
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I'm getting an error trying to index the hg19 as well.

I have all the .fa files from the chromosomes, I concatenated them into hg19.fa. I then run:

bwa index hg19.fa

and I get:

shakti:~/Documents/Bioinformatics/hg19 kmewis$ bwa index hg19.fa
[bwa_index] Pack FASTA... 70.84 sec
[bwa_index] Reverse the packed sequence... 38.55 sec
[bwa_index] Construct BWT for the packed sequence...
bwa(1791) malloc: *** vm_allocate(size=3095678976) failed (error code=3)
bwa(1791) malloc: *** error: can't allocate region
bwa(1791) malloc: *** set a breakpoint in szone_error to debug
Bus error

What could this mean? I'm running this on a PowerPC Mac with 16gb of RAM.

Thanks!
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Old 11-26-2010, 06:57 PM   #7
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What does file /path/to/bwa tell you? Was bwa generated as a 64 bits binary? It seems bwa failed while allocating memory.
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Old 11-29-2010, 11:32 AM   #8
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Quote:
Originally Posted by drio View Post
What does file /path/to/bwa tell you? Was bwa generated as a 64 bits binary? It seems bwa failed while allocating memory.
I don't know what file path/to/bwa is supposed to tell me, it says:

/path/to/bwa: cannot open (/path/to/bwa)

My bwa executable is in ~/bin.

How can I tell if it was generated as a 64 bit binary instead of a 32 bit? I just used the makefile that came with bwa 0.5.8a...
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Old 11-29-2010, 06:52 PM   #9
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What do you get when you run?:

Code:
$ file ~/bin/bwa
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Old 11-30-2010, 10:58 AM   #10
kmewis
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Here's the output:

shakti:~/Documents/Personal Stuff/Genome kmewis$ file ~/bin/bwa
/Users/kmewis/bin/bwa: Mach-O executable ppc

I'm using this on a PowerPC, so this is what I'd expect.
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Old 12-01-2010, 05:05 AM   #11
drio
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It seems is 32 bits binary. The file command reports 64 bits in a 64bit system. Have you tried any other aligner or tool that requires to address big chunks of memory?

Code:
$ file ./bwa
./bwa: Mach-O 64-bit executable x86_64
Also, it would be useful is you post here the gcc directives you used while compiling (output of make).
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Old 12-01-2010, 10:58 AM   #12
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I haven't tried any other tools yet, though I've heard that bowtie is another good aligner to use.

I just tried the other alignment option, BWT, and it seems to be doing alright now.

bwa index -a bwtsw hg19.fa

I read that this is for single end reads, which I assume is what the hg19 sequence I downloaded is.

Thanks so much for the help though; just knowing that someone out there is willing to help gives me more motivation to try to get it working! I appreciate it. I'm sure I'll have additional questions once I've got this going, but these forums are very helpful.
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Old 12-01-2010, 12:13 PM   #13
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Be careful with bwtsw. That's the algorithm for longer reads. It may not be what you are
looking for.
I
think your system is not 64bits. You will have the same issues with other tools. I suggest you spend some time figuring that out.
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Old 12-01-2010, 12:29 PM   #14
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I don't think my system is 64 bits either; is a 64 bit system required?

It's been a couple weeks since I made bwa. It seems to have made properly, it gave me the bwa.exe file as an output. I made a new directory to try to make bwa again to give you the output, but it seems to not be working. Output is:

shakti:~/Documents/bwa-0.5.8a kmewis$ makefile
/Applications/muscle3.6_src/makefile: line 12: CFLAGS: command not found
/Applications/muscle3.6_src/makefile: line 13: LDLIBS: command not found
/Applications/muscle3.6_src/makefile: line 16: OBJ: command not found
/Applications/muscle3.6_src/makefile: line 17: EXE: command not found
RM: =: No such file or directory
RM: rm: No such file or directory
RM: -f: No such file or directory
CP: =: No such file or directory
/Applications/muscle3.6_src/makefile: line 22: GPP: command not found
/Applications/muscle3.6_src/makefile: line 1: GPP: command not found
/Applications/muscle3.6_src/makefile: line 1: CFLAGS: command not found
LD: can't open: = (No such file or directory, errno = 2)
LD: no object files loaded
/Applications/muscle3.6_src/makefile: line 1: GPP: command not found
/Applications/muscle3.6_src/makefile: line 1: CFLAGS: command not found
powerpc-apple-darwin8-gcc-4.0.1: =: No such file or directory
powerpc-apple-darwin8-gcc-4.0.1: warning: '-x c' after last input file has no effect
powerpc-apple-darwin8-gcc-4.0.1: no input files
/Applications/muscle3.6_src/makefile: line 26: all:: command not found
/Applications/muscle3.6_src/makefile: line 1: wildcard: command not found

If I understand you correctly, you're saying the indexing of the database is different depending if I'm going to be comparing longer (Sanger, 454) reads instead of short (Illumina) reads? What would be different between the two?
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Old 12-01-2010, 02:59 PM   #15
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1. You have to address more than 4G of memory, a 32bit system won't allow you to do that.

2. run make not makefile

3. Yes. The mapping strategies are different. There are two different papers explaining
both algorithms (sort/long reads).
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Old 01-04-2011, 04:21 AM   #16
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Quote:
bwa index -a bwtsw /data/Bioinfo/genomes/hg18.fa

Here is the error:

[bwa_index] Pack FASTA... [bns_fasta2bntseq] fail to open file '/data/Bioinfo/genomes/hg18.fa.pac'. Abort!
Aborted
I met the same problem while building hg18 index,aborted!However,while coping with single chromosome it worked well.Does this mean insufficient memory?The total memory of the machine is 4GB.The manual says to build hg18 with command bwtsw requires only 2.5GB,then what's wrong with it?
Any help is appreciated!
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Old 01-08-2013, 08:42 AM   #17
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Hello,
Im having an index error as well. I am trying to index human genome build 37. I am using a Mac OS 10.5.8, 64 bit, 8GB of RAM and 280GB of space.
When I run the command:
bwa index -a bwtsw -p human_g1k_v37 human_g1k_v37.fasta

BWA starts indexing the genome but stops and provides an error message (error code=12)

BWTIncConstructFromPacked] 630 iterations done. 1740074246 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 1778041526 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 1811782918 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 1841768294 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 1868415350 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 1892095270 characters processed.
[bwt_gen] Finished constructing BWT in 688 iterations.
[bwa_index] 2010.81 seconds elapse.
[bwa_index] Update BWT... bwa(3627) malloc: *** mmap(size=3101806592) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Bus error

Any Help with this will be appreciated.

Thanks a bunch!
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Old 06-18-2013, 11:26 PM   #18
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So this seems to be the place for bwa errors, so ill just add mine, any help would be greatly appreciated.

I downloaded the human genome hg19, and was going to index it, started like this:
VirtualBox[bwa-0.7.5a] ./bwa index -a bwtsw ../hum_genome/hum_genome19.fa
[bwa_index] Pack FASTA...
28.35 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6191387966, availableWord=447648912
[BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999998 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999998 characters processed.
.
.
but at the end i get this
[BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed.
[bwt_gen] Finished constructing BWT in 687 iterations.
[bwa_index] 2953.98 seconds elapse.
[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 3095694032 bytes at bwtindex.c line 135: Cannot allocate memory

any suggestions???
thanks
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Old 06-19-2013, 04:03 AM   #19
GenoMax
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Quote:
Originally Posted by weirdkid View Post
So this seems to be the place for bwa errors, so ill just add mine, any help would be greatly appreciated.

I downloaded the human genome hg19, and was going to index it, started like this:
VirtualBox[bwa-0.7.5a] ./bwa index -a bwtsw ../hum_genome/hum_genome19.fa
[bwa_index] Pack FASTA...
28.35 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6191387966, availableWord=447648912
[BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999998 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999998 characters processed.
.
.
but at the end i get this
[BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed.
[bwt_gen] Finished constructing BWT in 687 iterations.
[bwa_index] 2953.98 seconds elapse.
[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 3095694032 bytes at bwtindex.c line 135: Cannot allocate memory

any suggestions???
thanks
How much RAM have you currently allocated to this virtual server? Is your virtual server using a 32-bit or 64-bit OS?
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Old 06-19-2013, 07:32 PM   #20
weirdkid
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I figured it out, just had to make more RAM for the vm, it was 4gb which i thought would be enough, but it worked when i make it just over 5gb.
thanks anyway
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