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Question: Error after upload bam file
0
gravatar for GPS
4.5 years ago by
GPS • 20
India
GPS • 20 wrote:

Hi All

I am going to upload the bam file in galaxy by get-data -> upload file but i will get the error after upload file

Error:

Traceback (most recent call last):
  File "/home/plus91/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 118, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/plus91/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/plus91/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
Aborted (core dumped)

 

please any one can tell me solution on this error

 

Thank You

GPS
galaxy bam • 3.4k views
ADD COMMENT • link •
written 4.5 years ago by GPS • 20

See also later duplicate question Error executing Bowtie2: bam_index_build2() not yet implemented

ADD REPLY • link written 4.1 years ago by Peter Cock • 1.4k
2
gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Have you installed the latest stable version from samtools? Please use the souceforge version, the svn version has a bug as far as I know.
ADD COMMENT • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

Yes, I get the same error Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented from samtools v1.1. It is a known bug, see https://github.com/samtools/samtools/issues/199 - I am looking at a hack to work around this: https://github.com/peterjc/picobio/blob/master/sambam/samtools_auto.py

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