Dear Galaxy dev team,

I try to use a tool allowing to sort a bam file with the "samtools sort -n" command. This tool works on BAM test files but when I run it on a real BAM file (of 3.5 G), I got an error named "error" (see attachment) ... this does not help me.

In the handler.log, the job is finished normally and I don't find the error line named "error". When I run the galaxy command directly on the server, it works. Is there a log file to follow more precisely the errors? Indeed, I don't find where the "error" comes from and so I can't resolve my problem.

Here my log files :


more galaxy_20175.e

    [bam_sort_core] merging from 34 files...

more galaxy_20175.ec

    0

more galaxy_20175.o

    [bam_index_core] the alignment is not sorted (HISEQ:123:HBFN8ADXX:1:1101:1341:3979): 24-th chr > 13-th chr
    [bam_index_build2] fail to index the BAM file.

These "errors" are not the problem, because I have the same on the BAM test files and they give no problem (I have a green box at the end of the run, only for tests data of course).
Moreover, I got the following lines in my wrapper to be sure that they are only warnings :

    <stdio>
        <regex match="fail to index"
        source="both"
        level="warning"
        description="Warning: fail to index the bam file" />
        <regex match="the alignment is not sorted"
        source="both"
        level="warning"
        description="Warning: the alignment is not sorted" />
    </stdio>

more metadata_results_HistoryDatasetAssociation_35900_PbjjDh

    [true, "Metadata has been set successfully"]

more handler0.log

    galaxy.jobs DEBUG 2015-03-03 10:06:25,824 (20175) Working directory for job is: /galaxy_data/job_working_directory/020/20175
    galaxy.jobs.handler DEBUG 2015-03-03 10:06:25,850 (20175) Dispatching to drmaa runner
    galaxy.jobs DEBUG 2015-03-03 10:06:25,943 (20175) Persisting job destination (destination id: sge)
    galaxy.jobs.handler INFO 2015-03-03 10:06:25,994 (20175) Job dispatched
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:06:26,584 (20175) submitting file /galaxy_data/job_working_directory/020/20175/galaxy_20175.sh
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:06:26,584 (20175) command is: samtools sort -n  /galaxy_data/files/028/dataset_28339.dat /galaxy_data/files/028/dataset_28631.dat ; mv /galaxy_data/files/028/dataset_28631.dat.bam /galaxy_data/files/028/dataset_28631.dat; return_code=$?; cd /data12/galaxy/galaxy-env/galaxy; /data12/galaxy/galaxy-env/galaxy/set_metadata.sh /galaxy_data/files /galaxy_data/job_working_directory/020/20175 . /data12/galaxy/galaxy-env/galaxy/universe_wsgi.ini /galaxy_data/tmp/tmp28hp1G /galaxy_data/job_working_directory/020/20175/galaxy.json /galaxy_data/job_working_directory/020/20175/metadata_in_HistoryDatasetAssociation_35900_vmNjk7,/galaxy_data/job_working_directory/020/20175/metadata_kwds_HistoryDatasetAssociation_35900_IHm6c9,/galaxy_data/job_working_directory/020/20175/metadata_out_HistoryDatasetAssociation_35900_CboGKT,/galaxy_data/job_working_directory/020/20175/metadata_results_HistoryDatasetAssociation_35900_PbjjDh,,/galaxy_data/job_working_directory/020/20175/metadata_override_HistoryDatasetAssociation_35900_XD1a0c; sh -c "exit $return_code"
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:06:26,585 (20175) native specification is: -q galaxy
    galaxy.jobs.runners.drmaa INFO 2015-03-03 10:06:26,818 (20175) queued as 160573
    galaxy.jobs DEBUG 2015-03-03 10:06:26,874 (20175) Persisting job destination (destination id: sge)
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:06:27,907 (20175/160573) state change: job is queued and active
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:06:35,538 (20175/160573) state change: job is running
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:12:10,200 (20173/160571) state change: job finished normally
    galaxy.datatypes.metadata DEBUG 2015-03-03 10:12:10,451 loading metadata from file for: HistoryDatasetAssociation 35898
    galaxy.jobs DEBUG 2015-03-03 10:12:10,547 job 20173 ended
    galaxy.datatypes.metadata DEBUG 2015-03-03 10:12:10,551 Cleaning up external metadata files
    galaxy.jobs.runners.drmaa DEBUG 2015-03-03 10:46:16,161 (20175/160573) state change: job finished normally
    galaxy.jobs DEBUG 2015-03-03 10:46:16,371 setting dataset state to ERROR
    galaxy.jobs DEBUG 2015-03-03 10:46:16,464 job 20175 ended

I don't know why galaxy give the "setting dataset state to ERROR" line.

In attachment, you can see "21 : Bam sorted" on the test file and the "20 : Sort BAM on data 17" on the real file. You can see that it's not the "[bam_index_core] the alignment is not sorted (HISEQ:123:HBFN8ADXX:1:1101:1341:3979): 24-th chr > 13-th chr
 
  [bam_index_build2] fail to index the BAM file." line which generate the error.

Thank you in advance for your help.

Have a nice day.

Best regards,