hartleys
commented
4 years ago 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 notifications@github.com 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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J-Calvelo
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