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JennaJ edited this page Feb 14, 2017 · 4 revisions

Sort Your Inputs

Many tools require inputs to be sorted in a specific way prior to use. The tool form help will often declare if sorting is required and the expected ordering.

Good news! Galaxy includes tools to do this sorting.

Sorting tools

  • SortSam Best choice for SAM/BAM
  • Sort BAM dataset Alternate choice for SAM/BAM
  • SortBED order the intervals Best choice for BED/Interval
  • Sort data in ascending or descending order Alternate choice for Tabular/BED/Interval/GTF
  • VCFsort Best choice for VFC
  • Tool Form Options for Sorting Some tools have a tool form option to sort inputs during job execution. This uses more resources but is a choice. Whenever possible, sort inputs before using tools, especially if jobs are failing for not enough memory resources.

Tools and Tool groups that require input sorting

Htseq_count

Example error on bug report.

job info: This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help.

How to sort?

Set this option to Yes: Force sorting of SAM/BAM file by NAME

If the job still fails for memory after sorting, Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at http://usegalaxy.org (Galaxy Main):

https://wiki.galaxyproject.org/Support

NGS: SAMTools (most)

Example error on bug report. Yours may differ. If there is a problem, try sorting first before reporting a bug.

job stdout: [samopen] SAM header is present: N sequences. [bam_index_core] the alignment is not sorted (display_dataset_name): A-th chr > B-th chr [bam_index_build2] fail to index the BAM file.

How to sort?

Try using Coordinate sort on the inputs with SortSam before using these tools. This is often required as a distinct step even if the input dataset states in the name that it is already sorted.

NGS: Picard (most)

Tools can error for a variety of reasons that seem to be unrelated to sort order, including this one seen on the bug report (click on the green bug icon, but there is no need to submit the bug/error):

job info: This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help.

If the job still fails for memory after sorting, Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at http://usegalaxy.org (Galaxy Main):

https://wiki.galaxyproject.org/Support

NGS: RNA-seq: Tophat, Cufflinks, Cuffmerge, Cuffdiff

Different errors can be reported and some may seem unrelated to sort order. Try sorting as a first pass troubleshooting solution.

If sorting does not work, it could be that your FASTQ data is not actually in .fastqsanger format. This occurs quite often in reported issues. For the quickest resolution, instead of reporting the bug and being sent back this link, first double check your data format directly using the guidelines in Section 2.11 of the Galaxy support wiki:

https://wiki.galaxyproject.org/Support

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