[carolW]

No to your first question.

Yes, I am admin of the machine

I tried to install the related package to limit, but seems that it's not complete

vlimit
vlimit: vc_get_task_xid(): Function not implemented
limit
No command 'limit' found, did you mean:
Command 'vlimit' from package 'util-vserver' (universe)
limit: command not found

[GenoMax]

No to your first question.

Not much left to try except to make sure that your copy of bwa is working right with a small dataset. You should try to find another machine with more memory.

[carolW]

I found the problem but the solution doesn't help and causes another problem:

When I uncompressed the index file from cufflinks web site, it created different folders, in one of them, there was a symbolic link to the index file. So I was using the symbolic link which caused the segfault.

Now I use the right index file but bwa samse is unable to locate the index file although the path is correct:

../pgm/bwa-0.7.3a/bwa samse ~/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa SRR062641.filt.sai SRR062641.filt.fastq > SRR062641.filt.sam
[bwa_sai2sam_se] fail to locate the index
[main] Version: 0.7.3a-r367
[main] CMD: ../pgm/bwa-0.7.3a/bwa samse ~/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa SRR062641.filt.sai SRR062641.filt.fastq

ls -lt /home/carolw/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
-rwxrwxr-x 1 carolw carolw 3157279232 Apr 26 10:52 /home/yasrebih/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

ls -lt /home/carolw/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/
total 3083296
-rwxrwxr-x 1 carolw carolw 3157279232 Apr 26 10:52 genome.fa
-rwxrwxr-x 1 carolw carolw 3099 Apr 13 2012 genome.dict
-rwxrwxr-x 1 carolw carolw 783 Mar 15 2012 genome.fa.fai

[carolW]

I don't know the following issue could be related to my bwa samse problem:

I tried to run gatk for local realignment of a bam file. I used a 1000genomes bam file and NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam that is recommended on gatk documentation. I have an incompatibles contigues between the input reads and the reference files (see below). Basically, in the reference file downloaded from the cufflinks website, chromosomes are annotated as chr_nbOfChr like chr1, chrX etc and in the bam file as 1, X etc.

Does it mean that because of this (problem with gatk and bwa samse), the index file downloaded from cufflinks is not really usable with different data sets although the problem types are different (location of index file and chr annotation)?

Look forward to your advices,

Carol
------------------------------------------------------
ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found.
##### ERROR reads contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605]
##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]