[holywoool]

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!

[eseq_prak]

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!

[weirdkid]

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

[GenoMax]

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?

[weirdkid]

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

[mmmm]

bwa index

BWA users- I get less than 8 output files when using BWA to index the reference genome- any explanation, please and would this affect BWA alignment?

bwa index reference.fna

[GenoMax]

BWA users- I get less than 8 output files when using BWA to index the reference genome- any explanation, please and would this affect BWA alignment?

bwa index reference.fna

Please post additional information about what OS (32/64-bit) you are using (virtual or real), amount of memory you have. Are there any error messages? I assume "reference.fna" is a multi-fasta file? Which files are you seeing (extensions)?

[mmmm]

the reference.fna is not a multi-fasta files. it is the complete bacterial genome.
I can see (.amb, .ann, .bwt, .pac, .sa) but can not see (.rpac, .rsa, .rbwt)

I have more than enough space on the server. there is no error message?

[GenoMax]

That looks right.

As of bwa version 0.6.x the forward and reverse indexes were merged, eliminating the .rxxx files.

[mmmm]

grateful thanks for clarification. Now, I am trying to detect the gene coverage cin the mapped reads compared to the reference genome using

bedtools
coverageBed -abam alignment.bam -b gff > coverage.txt

(but I have found that no genes have been mapped at all to the reference genome when opened the coverage.txt in a libreoffice)?

[GenoMax]

See the notes for "genomecov": http://bedtools.readthedocs.org/en/l...genomecov.html

Have you sorted your bam file?

[mmmm]

I did sort the bam file- should this be ok?

bedtools
coverageBed -abam sortedbam -b gff > coverage.txt

[GenoMax]

I did sort the bam file- should this be ok?

bedtools
coverageBed -abam sortedbam -b gff > coverage.txt

That should be ok. Are you not seeing anything in the coverage.txt file?

Do you want to try "multicov" along with a BED format file for the genes? http://bedtools.readthedocs.org/en/l.../multicov.html

[mmmm]

the coverage.txt file contains genes annotations (gff) but none of my aligned reads are covered by these annotated genes; I get (0) in the last column of the coverage.txt file for all genes

[GenoMax]

The "gff" in your command line above is the actual GFF format file for the annotations, correct (here if the format reference for GFF3: http://www.sequenceontology.org/gff3.shtml And the file actually matches the original genome used for alignment?

Have you checked your aligned bam file (using IGV for example) to make sure that the alignments look good?