Question: Galaxy can't find installed samtools when doing BWA mapping
0
yu.1.wang • 20 wrote:
Hello, I am trying a tutorial on NGS mapping. I installed BWA and samtools from tool_shed, but I got the following error:
Traceback (most recent call last):
File "/local/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/local/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation
File "/local/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
BWA: package_bwa_0_7_10_039ea20639
samtools: package_samtools_0_1_19 package_samtools_1_1 package_samtools_1_2
I used toolshed.g2.bx.psu.edu suit_samtools_1_2 and don't know why all the versions of samtools are installed.
Could this be the issue? Thanks,
Best,
Yu Wang
GALAXY TOOL ERROR REPORT
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This error report was sent from the Galaxy instance hosted on the server
"http://localhost:8080/galaxy/"
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This is in reference to dataset id 161 from history id 51
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You should be able to view the history containing the related history item
6: Map with BWA-MEM on data 1 and data 2 (mapped reads in BAM format)
by logging in as a Galaxy admin user to the Galaxy instance referenced above
and pointing your browser to the following link.
http://localhost:8080/galaxy/history/view?id=dff4190d282fb07a
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The user 'we' provided the following information:
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job id: 154
tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.2.1
tool version: 0.2.1
job pid or drm id: 6440
job tool version:
-----------------------------------------------------------------------------
job command line:
bwa mem -t "${GALAXY_SLOTS:-1}" -v 1 "/local/galaxy-dist/tool-data/hg19/bwa_mem_index/hg19/hg19.fa" "/home/galaxy/galaxy-dist/galaxy/database/files/000/dataset_157.dat" "/home/galaxy/galaxy-dist/galaxy/database/files/000/dataset_156.dat" | samtools view -Sb - > temporary_bam_file.bam && samtools sort -f temporary_bam_file.bam /home/galaxy/galaxy-dist/galaxy/database/files/000/dataset_161.dat
-----------------------------------------------------------------------------
job stderr:
-----------------------------------------------------------------------------
job stdout:
-----------------------------------------------------------------------------
job info:
Unable to finish job
-----------------------------------------------------------------------------
job traceback:
Traceback (most recent call last):
File "/local/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/local/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation
File "/local/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found