I need to build a color space index for the complete human genome build GRCh37 including the haplotypic chromosomes.
On the complete set (35 chromosomes) the BWA indexing fails, and seem to hang forever (>20 hrs) on converting the nt PAC to color PAC. I used the 'bwa index -c -a bwtsw 'fasta_file' option.
After playing a bit, removing 1 or 2 chromosomes from this set resolves the issue; actually when the nt.pac file is 1009 MB it works, but adding a chromosome and raising the nt.pac filesize to 1049 MB fails the indexing completely.
So there are no errors or chrashes with the complete build, but it just remains in building the cs version of the PAC file. We've tried this on several systems with 64 GB ram and plenty of disk space. Both version 0.5.1 and 0.5.5 seem to have this issue.
hopefully, this can be fixed.
On the complete set (35 chromosomes) the BWA indexing fails, and seem to hang forever (>20 hrs) on converting the nt PAC to color PAC. I used the 'bwa index -c -a bwtsw 'fasta_file' option.
After playing a bit, removing 1 or 2 chromosomes from this set resolves the issue; actually when the nt.pac file is 1009 MB it works, but adding a chromosome and raising the nt.pac filesize to 1049 MB fails the indexing completely.
So there are no errors or chrashes with the complete build, but it just remains in building the cs version of the PAC file. We've tried this on several systems with 64 GB ram and plenty of disk space. Both version 0.5.1 and 0.5.5 seem to have this issue.
hopefully, this can be fixed.
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