HomeCLC software: Important notificationsIssues affecting only older versions of productsWorkflows with Map Reads to Reference as the first step use only the first 120 selected elements

2.26. Workflows with Map Reads to Reference as the first step use only the first 120 selected elements

Issue Description

When running a workflow that contains the Map Reads to Reference tool as the first step, only the reads in the first 120 selected elements will be used. The only indication of this limitation is provided in the Workflow wizard where the (120) is shown even if more than 120 input elements are selected.

Analyses affected

Workflows containing the Map Reads to Reference tool as the first step are affected when more than 120 elements are selected. This includes when running such a workflow in batch mode, where one or more batch units contains more than 120 elements.

This issue does *not* affect workflows where the Map Reads to Reference tool is not the first step. While the limit of 120 input elements still exists, such a workflow will fail with an informative error if another workflow element passes more than 120 elements into the Map Reads to Reference tool.

If more than 120 data elements are supplied to the Map Reads to Reference tool when run from the Workbench Toolbox, (i.e. not within a workflow), the limit of 120 input elements exists, but a warning is shown in the wizard saying "At most 120 inputs are allowed. Create a new sequence list first."

Expected impact

Any read mapping generated in a workflow with Map Reads to Reference as the first workflow tool and more that 120 input files would be missing reads that were expected to be included, without obvious indication that this is the case.

Work arounds

1) Concatenate sequence elements or sequence lists into one or more sequence lists, such that fewer than 120 data elements contain all the reads to be mapped.

How can I concatenate sequence lists and when do I need to?

2) Generate several mappings, manually or using batching, using 120 or fewer input elements per mapping task. The resulting mappings could then be merged later, if desired.

Affected software

  • CLC Genomics Workbench 7.5 through 9.5.5, and versions 10.0 through 10.1.1.
  • Biomedical Genomics Workbench 2.1 through 3.5.5, and versions 4.0 through 4.1.1.

Affected analyses launched from the above workbenches to run on the CLC Genomics Server, version 6.5 through 8.5.5, and versions 9.0 through 9.1.1 are also affected.

 

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