I’m trying to do QC on my RNAseq samples, and after mapping with STAR (no gene counts, 2-pass, hg38 with GFF file for spli junctions) and passing the BAM file to Qualimap RNA-seq QC, I get a error.
The problem is that the program doesn’t even spit the error, as seen in the image.
Java memory size is set to 1200M
Launching application…
detected environment java options -Djava.awt.headless=true -Xmx7680m
QualiMap v.2.2.2-dev
Built on 2019-11-11 14:05
Selected tool: rnaseq
Initializing regions from features.gtf…
Initialized 1
"
Upon further inspection, this is the error:
"
Dataset Error Report
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/qualimap_rnaseq/qualimap_rnaseq/2.2.2d+galaxy1 .
Details
Execution resulted in the following messages:
Fatal error: Exit code 255 ()
Tool generated the following standard error:
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/031/100/31100658/_job_tmp -Xmx7g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/031/100/31100658/_job_tmp -Xmx7g -Xms256m
Failed to run rnaseq
java.lang.IllegalArgumentException: Comparison method violates its general contract!
at java.base/java.util.TimSort.mergeLo(TimSort.java:781)
at java.base/java.util.TimSort.mergeAt(TimSort.java:518)
at java.base/java.util.TimSort.mergeForceCollapse(TimSort.java:461)
at java.base/java.util.TimSort.sort(TimSort.java:254)
at java.base/java.util.Arrays.sort(Arrays.java:1441)
at org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler.createHelperMaps(TranscriptDataHandler.java:652)
at org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler.constructTranscriptsMap(TranscriptDataHandler.java:175)
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.loadRegionsFromGTF(ComputeCountsTask.java:702)
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.initRegions(ComputeCountsTask.java:608)
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:479)
at org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68)
at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:221)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
"
I’ve used the BAM file that STAR generates and the same GFF reference I used to align with STAR.
I’m getting a similar error when trying to run QualiMap BAM QC on a collection of mapped reads from RNA STAR. Format is bam, database is hg38. All jobs failed and I get the following tool error message: “Remote job server indicated a problem running or monitoring this job.” or on some jobs: “Failed to communicate with remote job server.”
My history is now filled with 11 failed jobs for each of the datasets in my collection (they all have the same name, see picture attached).
Am I getting the inputs wrong or what could be the reason?
@clsven, I’ve just tested QualiMap BamQC on small datasets with default parameters in both usegalaxy.org and usegalaxy.eu; the .org jobs didn’t even run, while .eu jobs ran perfectly in a short time.
I’d suggest you test the European instance and tell us if you have better luck.
What’s the best way to transfer my datasets (i.e. the entire collection) to the European server? Neither sharing the history with my .eu account, nor downloading a dataset from the URL seems to work.
@clsven, How exactly didn’t work? Can you show us the error? Are the files too big? You can also copy some datasets to a new history and download this whole history.
@clsven
UPDATE: The smaller datasets completed running ok in the .org instance, although it took much more time to start/complete. The bigger one is still running on .org. Also there are interesting differences about the org/eu runs:
Eu
has Command Line and Tool Standard Output text; Tool Standard Error empty:
I’ve contacted both admins about updating. This will happen in the near term. And the updated versions may resolve some of the problems reported (changes are mostly bug fixes + additional tool tests, and not all in the suite were updated, just a few of the tools).
Also, some reported metrics on the Job Details page can vary by Galaxy server. This may be due to admin settings, cluster types, or the version of Galaxy itself the server is running. Org has been upgraded to the pre-release of 21.05 (for testing). Eu is at the master 21.01 release. Releases — Galaxy Project 21.05.1.dev0 documentation
I’m going to bookmark this for an update. Plan to retest it all once updated – or may report the update and let people rerun to see if fixes their specific use case. If I don’t get back within a week or so, feel free to ping for an status update.
@David So when I try to share the history with the account e-mail address that I am registered with at the .eu instance, it says: “xxx is not a valid Galaxy user.”. Also, when I try to set permissions it doesn’t find my e-mail address (“No matches found”).
But fetching the data via the URL seems to works now. I had forgotten to make my history accessible.
