I have run the basic example from the manual:
java -Xmx4G -jar "/home/s1872081/QoRTs-STABLE.jar" QC --generatePlots --singleEnded "/home/s1872081/MScProject/RNA-seq/aligned/SRR5077600/SRR5077600_Aligned.sortedByCoord.out.bam" "/home/s1872081/MScProject/RNA-seq/genome/gencode.vM21.primary_assembly.annotation.gtf.gz" /home/s1872081/MScProject/RNA-seq/aligned/qc/SRR5077600/
The version I ma using:
Starting QoRTs v1.3.6 (Compiled Tue Sep 25 11:21:46 EDT 2018)
And got the bellow error. The bam files were generated with STAR and samtools flagstat does not crash while processing it.
Checking first 10000 reads. Checking SAM file for formatting errors...
============================FATAL_ERROR============================
QoRTs encountered a FATAL ERROR. For general help, use command:
java -jar path/to/jar/QoRTs.jar --man
============================FATAL_ERROR============================
Error info:
Exception in thread "main" java.lang.UnsupportedOperationException: empty.min
at scala.collection.TraversableOnce.min(TraversableOnce.scala:222)
at scala.collection.TraversableOnce.min$(TraversableOnce.scala:220)
at scala.collection.mutable.ArrayOps$ofByte.min(ArrayOps.scala:203)
at internalUtils.commonSeqUtils$.$anonfun$initSamRecordIterator$3(commonSeqUtils.scala:710)
at internalUtils.commonSeqUtils$.$anonfun$initSamRecordIterator$3$adapted(commonSeqUtils.scala:709)
at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:234)
at scala.collection.immutable.List.foreach(List.scala:389)
at scala.collection.TraversableLike.map(TraversableLike.scala:234)
at scala.collection.TraversableLike.map$(TraversableLike.scala:227)
at scala.collection.immutable.List.map(List.scala:295)
at internalUtils.commonSeqUtils$.initSamRecordIterator(commonSeqUtils.scala:709)
at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1031)
at qcUtils.runAllQC$.run(runAllQC.scala:970)
at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:680)
at runner.runner$.main(runner.scala:98)
at runner.runner.main(runner.scala)
This does not happen on bam file generated with bwa+samtools. Converting STAR bam to bam with samtools view does not help.
I have run the basic example from the manual: java -Xmx4G -jar "/home/s1872081/QoRTs-STABLE.jar" QC --generatePlots --singleEnded "/home/s1872081/MScProject/RNA-seq/aligned/SRR5077600/SRR5077600_Aligned.sortedByCoord.out.bam" "/home/s1872081/MScProject/RNA-seq/genome/gencode.vM21.primary_assembly.annotation.gtf.gz" /home/s1872081/MScProject/RNA-seq/aligned/qc/SRR5077600/
The version I ma using: Starting QoRTs v1.3.6 (Compiled Tue Sep 25 11:21:46 EDT 2018)
And got the bellow error. The bam files were generated with STAR and samtools flagstat does not crash while processing it.
Checking first 10000 reads. Checking SAM file for formatting errors... ============================FATAL_ERROR============================ QoRTs encountered a FATAL ERROR. For general help, use command: java -jar path/to/jar/QoRTs.jar --man ============================FATAL_ERROR============================ Error info: Exception in thread "main" java.lang.UnsupportedOperationException: empty.min at scala.collection.TraversableOnce.min(TraversableOnce.scala:222) at scala.collection.TraversableOnce.min$(TraversableOnce.scala:220) at scala.collection.mutable.ArrayOps$ofByte.min(ArrayOps.scala:203) at internalUtils.commonSeqUtils$.$anonfun$initSamRecordIterator$3(commonSeqUtils.scala:710) at internalUtils.commonSeqUtils$.$anonfun$initSamRecordIterator$3$adapted(commonSeqUtils.scala:709) at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:234) at scala.collection.immutable.List.foreach(List.scala:389) at scala.collection.TraversableLike.map(TraversableLike.scala:234) at scala.collection.TraversableLike.map$(TraversableLike.scala:227) at scala.collection.immutable.List.map(List.scala:295) at internalUtils.commonSeqUtils$.initSamRecordIterator(commonSeqUtils.scala:709) at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1031) at qcUtils.runAllQC$.run(runAllQC.scala:970) at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:680) at runner.runner$.main(runner.scala:98) at runner.runner.main(runner.scala)
This does not happen on bam file generated with bwa+samtools. Converting STAR bam to bam with samtools view does not help.