Hi,
This problem bellow is solved thanks to an eccho on $PATH and
$DRMAA_LIBRARY_PATH.
I have modified ~/.bash_profile file to define these two variables.
I just have another questio n about BWA : I try to map with BWA for
Illumina (reference and fastqsanger file) but I have this message :
BWA run on single-end
An error occurred running this job: entree dans bwa for illumina
BWA Version: 0.6.1-r104
BWA run on single-end dataEpilog : job finished at ven avr 6 14:16:01
CEST 2012
entree dans bwa wapper
Thanks in advance,
Sarah Maman
Sarah Maman a écrit :
Hi Nate,
When I operate on Genomic Intervals → Get Flanks. The user interface
for the tool will appear in the center panel. Make sure the dataset 2:
UCSC Main... is selected and set Length of Flanking region to 1000 to
create intervals 1000bp upstream of each gene.
I have this error :
Tool execution generated the following error message:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The tool produced the following additional output:
Skipped 2 invalid lines starting with #40094L "chr5_h2_hap1 281 935
NM_022909 0 + 281 377 0 1 654, 0,"
Location: Upstream, Region: whole, Flank-length: 1000, Offset: 0
Epilog : job finished at ven avr 6 13:59:08 CEST 2012
Moreover, when I Map with BWA for Illumina ( genome ref and fastq
fatsqsanger format ), I have this error :
Tool execution generated the following error message:
entree dans bwa wapperThe alignment failed.
Error aligning sequence. /bin/sh: bwa: command not found
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The tool produced the following additional output:
entree dans bwa for illumina
Could not determine BWA version
Epilog : job finished at ven avr 6 14:04:13 CEST 2012
Could you please help me ?
Thanks in advance,
Sarah Maman
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