bowtie-build failed to create alignment index

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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.com on 9 Jan 2015 at 5:03

[GoogleCodeExporter]

This is solved. I did not provide enough RAM (60G was enough but not 16)

Original comment by sara...@gmail.com on 19 Jan 2015 at 4:44

[GoogleCodeExporter]

Hi, 
As mentioned in the installation How to in the wiki source

My working Dir is : /chimerascan-0.4.5/chimerascan

i tried to build Index with follwing command
python chimerascan_index.py /MGMSTAR1/SHARED/RESOURCES/HG19_GENOME/hg19.fa 
Hg19_TrcsptomeAnntn /MGMSTAR1/SHARED/STAFF/KIRAN.P/chimerascan-0.4.5/chimerascan

but it threw Error is follows

Traceback (most recent call last):
  File "chimerascan_index.py", line 32, in <module>
    import chimerascan.pysam as pysam
ImportError: No module named chimerascan.pysam

how to Fix this i have all the installation steps correctly,,, What to be done 

Original comment by kira...@medgenome.com on 18 Jun 2015 at 7:50