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Question: Error executing Bowtie2: bam_index_build2() not yet implemented
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gravatar for Mikel Egaña Aranguren
4.1 years ago by
Mikel Egaña Aranguren • 10
Spain
Mikel Egaña Aranguren • 10 wrote:

I'm trying to execute Bowtie2 in Galaxy but I get the following Dataset generation error:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 118, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 959, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )  # call datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 244, in set_meta
    raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented

Any ideas of how to solve it? Thanks

 

 

 
metadata bowtie dataset generation datatypes bam • 4.8k views
ADD COMMENT • link •
modified 4.1 years ago by Bjoern Gruening ♦ 5.1k • written 4.1 years ago by Mikel Egaña Aranguren • 10

Duplicate of Error after upload bam file

ADD REPLY • link written 4.1 years ago by Peter Cock • 1.4k
3
gravatar for Bjoern Gruening
4.1 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Mikel,

it's just a guess. Have you samtools > 1.0 installed? Galaxy uses samtools to index BAM files for you, but I'm not sure samtools > 1.0 is supported. Can you try to install samtools < 1 and try again?

Ciao,

Bjoern
ADD COMMENT • link written 4.1 years ago by Bjoern Gruening ♦ 5.1k
1

Known bug in samtools, see https://github.com/samtools/samtools/issues/199

ADD REPLY • link written 4.1 years ago by Peter Cock • 1.4k

Yes, using a local samtools 0.1.19 worked, many thanks!

ADD REPLY • link written 4.1 years ago by Mikel Egaña Aranguren • 10
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