error in creating reference

[Jeremy Wu]

deFuse: 0.6.1
gmap: GMAP version 2014-05-30
Ensemble version in the config file:
ensembl_version = 74
ensembl_genome_version = GRCh37
ucsc_genome_version = hg19

Error message:

Reading gene models
Creating bowtie indices
Creating samtools fasta indices
Splitting est file
Creating 2bit files
Creating cdna gmap index
Failure for defuse command:
/home/hbi16088/bin/gmap_build -D /home/hbi16088/data/defuse_dataset_75/gmap -d cdna -o /home/hbi16088/data/defuse_dataset_75/gmap/Makefile.cdna.tmp /home/hbi16088/data/defuse_dataset_75/defuse.cdna.fa
Reason:
Job command with nonzero return code
Job output:
Running on hbiarray01.h3b.hope
Unknown option: o
-k flag not specified, so building with default 15-mers
Sorting chromosomes in chrom order. To turn off or sort other ways, use the -s flag.
Creating files in directory /home/hbi16088/data/defuse_dataset_75/gmap/cdna
Running /home/hbi16088/bin/fa_coords -o /home/hbi16088/data/defuse_dataset_75/gmap/cdna.coords -f /home/hbi16088/data/defuse_dataset_75/gmap/cdna.sources
Can't open file /home/hbi16088/data/defuse_dataset_75/gmap/Makefile.cdna.tmp at /home/hbi16088/bin/fa_coords line 209.
Opening file /home/hbi16088/data/defuse_dataset_75/gmap/Makefile.cdna.tmp
/home/hbi16088/bin/fa_coords -o /home/hbi16088/data/defuse_dataset_75/gmap/cdna.coords -f /home/hbi16088/data/defuse_dataset_75/gmap/cdna.sources failed with return code 512 at /home/hbi16088/bin/gmap_build line 230.

real    0m2.199s
user    0m0.070s
sys 0m0.028s

Return codes: 25
Commands failed after 6 seconds

[Andrew]

I believe this is fixed in the development version on bitbucket:
https://bitbucket.org/dranew/defuse