What steps will reproduce the problem?
pgm=~/bin/Chimerascan/chimerascan-0.4.5/bin/chimerascan_index.py
genome=/users/rg/projects/references/Genome/H.sapiens/hg19/Homo_sapiens.GRCh37.c
hromosomes.chr.M.fa
module purge
module load Bowtie/0.12.7-goolf-1.4.10-no-OFED
time python $pgm $genome hg19.ucsc_genes.txt hg19_ucsc_genes_Index 2>
hg19_ucsc_genes_Index/chimerascan_index_ucscgenes.err >
hg19_ucsc_genes_Index/chimerascan_index_ucscgenes.out
What is the expected output? What do you see instead?
The chimerascan index. I do not see it, but those files:
ll hg19_ucsc_genes_Index/
total 4.6G
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 17M Jan 9 15:44 gene_features.txt
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 3.2G Jan 9 15:44 align_index.fa
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 2.7M Jan 9 15:45 align_index.fa.fai
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 730M Jan 9 15:46 align_index.4.ebwt
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 651K Jan 9 15:46 align_index.3.ebwt
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 0 Jan 9 15:46 align_index.2.ebwt
What version of the product are you using? On what operating system?
chimerascan-0.4.5 on Linux ant-login5.linux.crg.es 2.6.32-504.1.3.el6.x86_64 #1
SMP Tue Nov 11 14:19:04 CST 2014 x86_64 x86_64 x86_64 GNU/Linux
Please provide any additional information below.
I ran the chimerascan indexer with the ucsc gene file provided here, the hg19
genome without haplotypes and Bowtie 0.12.7, and I get the following error
message after several minutes:
[fai_load] build FASTA index.
2015-01-09 15:45:21,906 - root - INFO - Building bowtie index
2015-01-09 16:04:02,486 - root - ERROR - bowtie-build failed to create
alignment index
together with a core.
Any idea why?
Original issue reported on code.google.com by
sara...@gmail.comon 9 Jan 2015 at 5:03