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Last updated 12-11-17

Check individual linked tickets to review the most current status for any known issue

Working at Galaxy Main https://usegalaxy.org?

Server-specific issues: https://github.com/galaxyproject/usegalaxy-playbook/issues

Issue by tool name

  1. (15) Heatmap 1.0.0 Missing dependencies. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3030
  2. (2 bugs +github) CummeRbund 1.0.1 Select for "gene_id" problematic. Graphs for Heatmap and Volcano plots also problematic. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/340
  3. (1) SnpEff Download v4.1.0 and 4.3k.0. Index problem for certain databases nested in .zip archives from the source. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/1354
  4. (many) Upload Retested 6/1/17 v 17.05 then again on 10/18/17 v 17.09 on Main. Still assigning "pileup" as autodetected datatype in a greedy way for tabular format data that has a variable numbers of columns per line. Impacts Galaxy Test and Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3001
  5. Rerun Function (many tools) Rerun view for grey "new" status dataset, and sometimes green successful datasets, fails to open Advanced Options on reloaded tool form. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2502
  6. (many) Htseq-count 0.6.1galaxy3 Does not report standardized memory failure error message. Suggested improvements are in the ticket. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2532
  7. (a few) Featurecounts Is being updated from 1.4.6.p5 to 1.5.3 to address a bug is but not in the MTS yet (was just upgraded). Update Main once in MTS and test. Impacts Galaxy Main https://usegalaxy.org. Details: https://github.com/galaxyproject/usegalaxy-playbook/issues/52

retest/status in progress

  1. (1) Annovar 0.2 Wrapper problems. Use v 0.1 as a workaround. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/4001
  2. (1) Picard SamToFastq 1.136.0 Does not list fastqsanger output datasets in Workflow editor. Impacts Galaxy Main http://usegalaxy.org and a local Galaxy (not tested on Cloudman). Details: https://github.com/galaxyproject/tools-devteam/issues/414
  3. (?) BWA-MEM 0.7.12.1 produces BAM that fails ValidateSamFile 1.136.0. Default options for both. ValidateSamFile tool needs tuning? Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2846

Note: (N) is number of confirmed bug reports about issue. Not all issues can be counted this way. Count of (many) indicates that this is ongoing user problem with usage, often clarified when reviewing other bug reports/questions.

Tools that need updated usage/help

Fixed pending server update

  1. (many) StringTie 1.3.3. Errors when output for DEseq2/EdgeR is selected. Impacts Galaxy Main http://usegalaxy.org. Details and workaround: https://github.com/galaxyproject/tools-iuc/issues/1322. Status: https://github.com/galaxyproject/usegalaxy-playbook/issues/60

Integration tests in progress ( v 17.09 )

TOOLS

  1. (21) MEME 4.11.1.0 Has dependency issues. Updates have not resolved usage problems yet (tool has never worked). Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1913
  2. Needs RE-TEST (many) Upload (across releases) Trailing return characters in pasted data cause problems and the "why" is not clear to users. Impacts Galaxy Main, locals, cloud. Details: https://github.com/galaxyproject/galaxy/issues/2886
  3. Needs RE-TEST (many) MAF tools 1.0.1 Switching between MAF data sources does not refresh tool form/dbkey list. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2828.

UI

  1. Needs RE-TEST (many) Pileup datasets not recognized by downstream tools. This is due to tabular datatype assignment by Mpileup/Generate pileup (SAMTools). Assignment of both start and end to the same column could be why auto-assignment of type is not possible. Workaround: Click on dataset's pencil icon and assign pileup datatype. Details: https://github.com/galaxyproject/galaxy/issues/1744
  2. Workflows NOTE that a new workflow form is pending and these usage issues will be re-tested. Behavior: Reference genome selection at runtime or changes through editor are not persistent or do not allow use of a Custom Reference Genome/Build. Known issues, sometimes linked to specific tools (SAMTool, Tophat). Impacts Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1132

Issue by user interface behavior

  1. Reference Genome Missing from tool First, make certain that the dataset has the "database" metadata asssignment. If still missing, the genome may be undergoing indexing (on Test, to be promoted to Main ). Check the details ticket below for notes and progress. If you do not see your genome, request it as instructed in the ticket. Remember that a Custom Reference Genome can be used right now instead for most tools. Impacts Bowtie2 Tophat(2) BWA BWA-MEM Kraken. Details: https://github.com/galaxyproject/galaxy/issues/1470

Issue with performance at Galaxy Main

  1. If there are issues with delays, reports of histories not loading, a blue screen stating that Galaxy is busy ... then check the Galaxy Status page to see if there is a problem with the server first: https://status.galaxyproject.org/
  2. If status is OK, then read recent posts at Galaxy Biostars, where transient issues are often reported and clarified. A new question can be asked if there is no activity about the problem. https://biostar.usegalaxy.org/

Issue by error message

  1. Error from a tool in the NGS: SAMtools or NGS: Picard groups about sort order.
  2. Tool is failing for memory or walltime (click on bug icon to review - this does not need to be submitted).
  3. Tool is failing for what appears to be a cluster error.
  4. Tool is failing and you are not sure what the error message means or how to troubleshoot/get help.

Try this first: Sort your inputs

Check all inputs: All Support help

If you cannot determine the problem from the help above, the bug report can be sent in: Common tool errors and solutions, including how to send in a bug report.

Correction Completed History

  1. Convert BIOM 2.1.5.0 Dependency issues (now resolved). Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/usegalaxy-playbook/issues/63
  2. Workflows Multiple input modifications within the editor triggers a browser crash. Impacts Galaxy Main http://usegalaxy.org (and potentially other Galaxy flavors). Details: https://github.com/galaxyproject/galaxy/issues/2835
  3. Upload Fixed early 2017. Tool was problematically padding spaces to tabs when number of pasted columns varies. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2602
  4. Uniprot Dependency fix on 5/15/17. Impacted Galaxy Main http://usegalaxy.org, locals, cloud (any install). Details: https://github.com/galaxyproject/galaxy/issues/3721
  5. Megablast 1.2.0. Fails for configuration error. Metagenomic alternative: Kraken. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/4498
  6. Freebayes 0.4.1 + 1.0.2.29-3 Now requires upsteam inputs have database metadata assigned - see ticket for workaround. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/409
  7. Du Novo: Align families 0.7 Tool updates removed the cluster targetting for Jetstream. Fix made (increased allocated resources at target clusters). Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3057
  8. Kraken 0.10.6, Krona pie chart from taxonomic profile 2.6.0, Convert Kraken data to Galaxy taxonomy representation 1.1 Missing dependencies, some localized to the roundup cluster (default). Resolved in updated tools and versions (Kraken 1.2, Krona 2.6.1). Impacts Galaxy Main http://usegalaxy.org. https://github.com/galaxyproject/galaxy/issues/3556
  9. GenomeDiversity PrepareInput gd_prepare_population_structure 1.1.0 Dependency/config issue resolved 1.2.0. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/4108
  10. DEXseq 1.20.1 Dependencies issues. Related tool DEXSeq Counts 1.20.1 already has fixed dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3709
  11. MACS2 bdgdiff + bdgbroadcall 2.1.1.20160309.0 Tool version updated 4/11/17 errors with "macs2 command not found". Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2226
  12. MACS2 bdgdiff 2.1.0.20151222.0 Did not have "Versions" menu on tool form. Cannot change versions on tool form still, but closed out anyway. Impacts Galaxy Main http://usegalaxyorg. Details: https://github.com/galaxyproject/galaxy/issues/3925
  13. Cuffmerge v 2.2.1 Older v 0.0.6 is successful with same inputs. Closed unless reported again. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2989 Might be related to https://github.com/galaxyproject/tools-iuc/issues/988
  14. DEXseq Count 1.20.1 Dependencies issues. Primary tool DEXSeq may also have the problem, but since the upstream tool is non-functional, it cannot be tested on Main. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3709
  15. Deseq2 2.11.38 MTS update to 2.11.39 fixes dependency issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/4046
  16. Deprecated tool Draw phylogeny 1.0.0 Version 1.0.0 has a dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3158
  17. Diffbind 2.2.0/2.1.0 Dependency problems fixed in 2.2.0 Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2318
  18. Salmon 0.7.2 Fails with a specific error message due to tool dependency problems. The updated tool version 0.8.2 resolved the problem. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3660
  19. Deep Tools correctGCBias Unrecognized arg --filterOut produces an error. Impacts Galaxy Main http://usegalaxy.org but is core tool issue. Details: https://github.com/fidelram/deepTools/issues/434
  20. Deep Tools multiBamSummary Doesn't always produce output. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/fidelram/deepTools/issues/436
  21. Tophat Tool is being deprecated and no longer runs on Jetstream (where original metadata problem was from). Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2838
  22. MAF tools 1.0.1 Fix made for legacy env updates. Extract Pairwise MAF blocks 1.0.1 https://github.com/galaxyproject/galaxy/issues/3934. GeneBed_Maf_Fasta2. (https://github.com/galaxyproject/galaxy/pull/3931). Tool Extract Pairwise MAF blocks may also need fix. Impacts Galaxy Main http://usegalaxy.org, locals, cloud.
  23. Trimmomatic Update to version 0.36.3 corrected tool form option "Illumina Clip" failures. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3691
  24. Picard Tool: CollectRnaSeqMetrics 1.136.0 Impacts Galaxy Main http://usegalaxy.org. Original Details: https://trello.com/c/XXlFa5ZL. Still fails with updated tool version 1.136.0. Update: Error due to input format - is very specific and needs to be clarified on tool form, see ticket. https://github.com/galaxyproject/galaxy/issues/1710.
  25. MarkDuplicatesWithMateCigar 1.126.0 Problem with tool form option specific to version 1.126.0. Repo updated to version 1.136.0 and now works at Main. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/401
  26. Trackster and GFF/GTF datasets Fail to load with a specific error. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3499
  27. EBI SRA Main 1.0.1 Tool errors when loading .bz2 compressed data from the "Submit files (galaxy)" link. Details and workaround: https://github.com/galaxyproject/galaxy/issues/1709
  28. Trackster and BED datasets Fail to load with a specific error. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1722
  29. DESEQ2 2.1.8.3 Fails after tool update - new error message in linked ticket. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/988 Might be related to https://github.com/galaxyproject/galaxy/issues/2989
  30. MACS2 Callpeak Errors out but job produces result data (in red datasets). Impact Galaxy Main http://usegalaxy.org and possibly other installs. Details: https://github.com/galaxyproject/tools-iuc/issues/1033
  31. MACS2 CallPeak This tool has a current known issue with the option Fold Enrichment. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/583
  32. NCBI SRA Tools Dependency/config issue resolved, but tool version mismatch for wrapper on Main. Smaller files working on a local, but not Main. Work-around: Use "Get Data > EBI SRA" or download from NCBI/FTP to Galaxy. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2533
  33. Deeptools Fails for a specific error. Tool has been revised and pending upgrade. Impacts Galaxy Main http://usegalaxy.org. Details and link to work-around posted at Galaxy Biostars: https://github.com/galaxyproject/galaxy/issues/2331. Other issues with tool at Galaxy Main, perhaps global (see ticket) https://github.com/galaxyproject/tools-iuc/issues/835
  34. Convert Formats: Convert BAM to ScIdx Fails for dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2460
  35. Group Fails under specific conditions. Fixed, pending deployment. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/pull/2166
  36. Multi-join Has dependencies issues. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2511
  37. GenomeDiversity Admixture gd_specify 1.1.0 Dependency/config issue corrected on server, no version change, retested after other GD 1.2.0 tools updated = pass. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2641
  38. BAMTools Convert, Merge, Randomize Fails for Convert to Bed + Yaml. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/378
  39. VCF-VCFintersect Needs to be updated in the Main Tool Shed and Galaxy Test/Main servers. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/391
  40. Bedtools SpacingBed Dependency/config issues. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2640
  41. Tophat Fails for a specific use case. Update to v 2.1.0 may solve (update: did solve). Also covers tool form option modeling. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/365
  42. Duplicates in UI Display of Tabular Datasets Fixed, pending deployment. Impacts Galaxy Main http://usegalaxy.org and all other Galaxy flavors. Details: https://github.com/galaxyproject/galaxy/pull/2527
  43. Multi-join Frozen tool form options (related to icon display, see linked issues in ticket). Impacts Galaxy Main http://usegalaxy.com. Details: https://github.com/galaxyproject/galaxy/issues/2512
  44. Fetch Alignments/Sequences MAF tools have a dependency issue. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2187
  45. Summary Statistics Fails for dependency issue. Impact http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2210
  46. CloudMap: "Hawaiian Variant Mapping with WGS" Dependency issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2304
  47. HISAT2 Fails, updating tool repo version on Main in progress. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2246
  48. Tophat Execution with a single fastq file (unpaired) produces an error. Wrapper or dependency issue. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2155
  49. Picard Tool: ValidateSamFile Errors (as a green successful dataset) in summary mode. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/369
  50. FastQC, MACS2 HTML results do not display when "eye" icon used. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2240
  51. Trim leading or trailing characters Fails when option to specify input is fastq is used. Impacts Galaxy Main http://usegalaxy.org and possibly locals running 16.04. Details and workaround: https://github.com/galaxyproject/galaxy/issues/2245
  52. CollectAlignmentSummaryMetrics Fixed on Main at version 1.136.0. https://github.com/galaxyproject/galaxy/issues/1692