"IMMPOSSIBLE STATE! FATAL ERROR!" with Hisat2 data - Bioconda installation #79
Comments
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Woah. So usually when I put an "impossible state" error it definitely means
that there is something really wrong that I didnt think was possible.
On first glance my guess would be that maybe some sort of IO issue?
Is it consistant? If you run it again exactly the same do you get the same
result?
Also useful would be the full log. That will include the version
information and the jvm version info and stuff like that, which can be
useful to narro wes things down...
…On Thu, Apr 23, 2020, 7:24 PM J-Calvelo ***@***.***> wrote:
Hello, I was trying to get splice junction counts from a Hisat2 alignment
with the following line:
qorts QC --maxReadLength 101 --nameSorted --minMAPQ 50 test.bam
wombase.gtf Count_Outputs
And got the following error:
Finished` reading SAM. Read: 11186385 reads/read-pairs.
Finished reading SAM. Used: 11039996 reads/read-pairs.
[Time: 2020-04-23 19:48:26] [Mem usage: [723MB / 1062MB]] [Elapsed Time: 00:22:50.0545]
> Read Stats:
> READ_PAIR_OK 11039996
> TOTAL_READ_PAIRS 11186385
> DROPPED_NOT_PROPER_PAIR 146389
> DROPPED_READ_FAILS_VENDOR_QC 0
> DROPPED_MARKED_NOT_VALID 0
> DROPPED_CHROMS_MISMATCH 0
> DROPPED_PAIR_STRANDS_MISMATCH 0
> DROPPED_IGNORED_CHROMOSOME 0
> DROPPED_NOT_UNIQUE_ALIGNMENT 0
> DROPPED_NO_ALN_BLOCKS 0
> DROPPED_NOT_MARKED_RG -1
Pre-alignment read count unknown (Set --seqReadCt or --rawfastq)
Writing Output...
<====== FATAL ERROR! ======>
----------------------------
Error message: "IMMPOSSIBLE STATE! FATAL ERROR! qcJunctionCounts.writeOutput, writing forSpliceSeq"
Stack Trace:
java.base/java.lang.Thread.getStackTrace(Thread.java:1606)
internalUtils.Reporter$.error(Reporter.scala:294)
qcUtils.qcJunctionCounts.$anonfun$writeOutput$3(qcJunctionCounts.scala:203)
qcUtils.qcJunctionCounts.$anonfun$writeOutput$3$adapted(qcJunctionCounts.scala:194)
scala.collection.Iterator.foreach(Iterator.scala:929)
scala.collection.Iterator.foreach$(Iterator.scala:929)
scala.collection.AbstractIterator.foreach(Iterator.scala:1417)
scala.collection.IterableLike.foreach(IterableLike.scala:71)
scala.collection.IterableLike.foreach$(IterableLike.scala:70)
scala.collection.AbstractIterable.foreach(Iterable.scala:54)
qcUtils.qcJunctionCounts.writeOutput(qcJunctionCounts.scala:194)
qcUtils.runAllQC$.$anonfun$runOnSeqFile$8(runAllQC.scala:1410)
qcUtils.runAllQC$.$anonfun$runOnSeqFile$8$adapted(runAllQC.scala:1410)
scala.collection.Iterator.foreach(Iterator.scala:929)
scala.collection.Iterator.foreach$(Iterator.scala:929)
scala.collection.AbstractIterator.foreach(Iterator.scala:1417)
scala.collection.IterableLike.foreach(IterableLike.scala:71)
scala.collection.IterableLike.foreach$(IterableLike.scala:70)
scala.collection.AbstractIterable.foreach(Iterable.scala:54)
qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1410)
qcUtils.runAllQC$.run(runAllQC.scala:960)
qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:672)
runner.runner$.main(runner.scala:97)
runner.runner.main(runner.scala)
<==========================>
Exception in thread "main" java.lang.Exception: IMMPOSSIBLE STATE! FATAL ERROR! qcJunctionCounts.writeOutput, writing forSpliceSeq
at internalUtils.Reporter$.error(Reporter.scala:299)
at qcUtils.qcJunctionCounts.$anonfun$writeOutput$3(qcJunctionCounts.scala:203)
at qcUtils.qcJunctionCounts.$anonfun$writeOutput$3$adapted(qcJunctionCounts.scala:194)
at scala.collection.Iterator.foreach(Iterator.scala:929)
at scala.collection.Iterator.foreach$(Iterator.scala:929)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1417)
at scala.collection.IterableLike.foreach(IterableLike.scala:71)
at scala.collection.IterableLike.foreach$(IterableLike.scala:70)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at qcUtils.qcJunctionCounts.writeOutput(qcJunctionCounts.scala:194)
at qcUtils.runAllQC$.$anonfun$runOnSeqFile$8(runAllQC.scala:1410)
at qcUtils.runAllQC$.$anonfun$runOnSeqFile$8$adapted(runAllQC.scala:1410)
at scala.collection.Iterator.foreach(Iterator.scala:929)
at scala.collection.Iterator.foreach$(Iterator.scala:929)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1417)
at scala.collection.IterableLike.foreach(IterableLike.scala:71)
at scala.collection.IterableLike.foreach$(IterableLike.scala:70)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1410)
at qcUtils.runAllQC$.run(runAllQC.scala:960)
at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:672)
at runner.runner$.main(runner.scala:97)
at runner.runner.main(runner.scala)
Not sure of what could have caused it. If its informative, I'm studying SL
trans-splicing and for this alignments I removed the splicer leader
sequences prior to the alignment so reads were hard trimmed.
Thanks
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Seems to be consistent and happens with other samples. Maybe there is something wrong with the conda version? |
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It looks like your flattened GFF has some sort of malformation. This can happen if your input GTF has special characters in one or more of the gene IDs. In particular the colon character ":" will break geneIDs. Could you send the GTF file? Or maybe just check the geneIDs? |
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Sorry for the delay, that seems to be the issue. I got the original GFF3 from wormbase and then processed it with gffread. Thanks |
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Ah. Ok. The problem is that colons are being used in the transcriptIDs and geneIDs. This problem is a carryover from the way DEXSeq generates UIDs for each entry. I thought I built in a check for this but apparently not. There are a couple different options. Easiest option would be to do a text-replace for the colons in the GFF3: zcat mygff.gff.gz | sed 's/[:]/-/g' > myFixedGff.gff.gz |
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Hello, I was trying to get splice junction counts from a Hisat2 alignment with the following line:
qorts QC --maxReadLength 101 --nameSorted --minMAPQ 50 test.bam wombase.gtf Count_OutputsAnd got the following error:
Not sure of what could have caused it. If its informative, I'm studying SL trans-splicing and for this alignments I removed the splicer leader sequences prior to the alignment so reads were hard trimmed.
Thanks
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