QoRTs error after aligning with STAR

[ghost]

Hello Hartley, I am getting this QoRTs error after cleaning the data by Trimmomatic and aligning the pair-ends reads by STAR. Please let me know where I am going wrong. I really appreciate your help.
My commands:-

java -Xmx16G -jar /work/LAS/vollbrec-lab/sharmistha/QoRTs.jar QC --generatePlots --stranded --verbose --maxReadLength 90 --genomeFA /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.fna.gz --rawfastq /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz,/work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz --generateSeparatePlots --outfilePrefix ${output} --chromSizes /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt --addFunctions mismatchEngine,annotatedSpliceExonCounts,FPKM,writeGeneBodyIv,fastqUtils,referenceMatch,writeDocs,makeJunctionBed,makeAllBrowserTracks,calcDetailedGeneCounts /work/LAS/vollbrec-lab/sharmistha/star_files/star_output_files/NB-rep-1_ATCACG_L001/${input1} /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/${output}/

Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017)
Starting time: (Mon Jul 02 14:04:41 CDT 2018)
INPUT_COMMAND(QC)
INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_files/star_output_files/NB-rep-1_ATCACG_L001/NB-rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam
INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz
INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned/
INPUT_ARG(generatePlots)=true
INPUT_ARG(stranded)=true
INPUT_ARG(verbose)=true
INPUT_ARG(maxReadLength)=Some(90)
INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.fna.gz))
INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz))
INPUT_ARG(generateSeparatePlots)=true
INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned
INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt)
INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, makeJunctionBed, makeAllBrowserTracks, calcDetailedGeneCounts)
Created Log File: /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.6JZ9kTs4cAFB.log
Starting QC
[Time: 2018-07-02 14:04:41] [Mem usage: [73MB / 2024MB]] [Elapsed Time: 00:00:00.0000]
QoRTs is Running in paired-end mode.
QoRTs is Running in any-sorted mode.
Chromosome size file added. Adding target wiggle plot generation.
Raw fastq files specified. Adding fastq testing.
Parameter --genomeFA found. Adding reference mismatch testing.
Running functions: CigarOpDistribution, FPKM, GCDistribution, GeneCalcs, InsertSize,
JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck,
annotatedSpliceExonCounts, calcDetailedGeneCounts,
chromCounts, cigarLocusCounts, fastqUtils,
makeAllBrowserTracks, makeJunctionBed, makeWiggles,
mismatchEngine, overlapMatch, readLengthDistro,
referenceMatch, writeBiotypeCounts, writeClippedNVC,
writeDESeq, writeDEXSeq, writeDocs, writeGeneBody,
writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody,
Checking first 10000 reads. Checking SAM file for formatting errors...
Stats on the first 10000 reads:
Num Reads Primary Map: 9103
Num Reads Paired-ended: 10000
Num Reads mapped pair: 9098
Num Pair names found: 4797
Num Pairs matched: 4301
Read Seq length: 36 to 90
Unclipped Read length: 36 to 90
Final maxReadLength: 90
maxPhredScore: 41
minPhredScore: 2
NOTE: Read length is not consistent.
In the first 10000 reads, read length varies from 36 to 90 (param maxReadLength=90)
Note that using data that is hard-clipped prior to alignment is NOT recommended, because this makes it difficult (or impossible) to determine the sequencer read-cycle of each nucleotide base. This may obfuscate cycle-specific artifacts, trends, or errors, the detection of which is one of the primary purposes of QoRTs!In addition, hard clipping (whether before or after alignment) removes quality score data, and thus quality score metrics may be misleadingly optimistic. A MUCH preferable method of removing undesired sequence is to replace such sequence with N's, which preserves the quality score and the sequencer cycle information.
Note: Data appears to be paired-ended.
Sorting Note: Reads are not sorted by name (This is OK).
Sorting Note: Reads are sorted by position (This is OK).
Done checking first 10000 reads. No major problems detected!
Starting getSRPairIterResorted...
SAMRecord Reader Generated. Read length: 90.
[Time: 2018-07-02 14:04:44] [Mem usage: [285MB / 2552MB]] [Elapsed Time: 00:00:03.0401]
Starting fastq readthrough.

Init FastqGC Utility
Init FastqQualityScore Utility
Init FastqNVC Utility
============================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.ArrayIndexOutOfBoundsException: 100
at qcUtils.fqcGC.runOnReadPair(fqcGC.scala:43)
at qcUtils.runAllQC$.$anonfun$runOnSeqFile$5(runAllQC.scala:1187)
at scala.collection.Iterator.foreach(Iterator.scala:929)
at scala.collection.Iterator.foreach$(Iterator.scala:929)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1417)
at scala.collection.IterableLike.foreach(IterableLike.scala:71)
at scala.collection.IterableLike.foreach$(IterableLike.scala:70)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at qcUtils.runAllQC$.$anonfun$runOnSeqFile$4(runAllQC.scala:1187)
at qcUtils.runAllQC$.$anonfun$runOnSeqFile$4$adapted(runAllQC.scala:1186)
at scala.collection.Iterator.foreach(Iterator.scala:929)
at scala.collection.Iterator.foreach$(Iterator.scala:929)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1417)
at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1186)
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)

[hartleys]

It looks like you set maxreadlength too low. It looks like there is a 100bp read somewhere in there. Are you sure the max read length is actually 90? That's the longest length found in the first 10k reads, but it looks like you're using variable trimming (which I generally recommend doing AFTER qorts qc testing, by the way).

…

On Mon, Jul 2, 2018, 3:27 PM SHARMISTHA CHAKRABORTTY < ***@***.***> wrote: Hello Hartley, I am getting this QoRTs error after cleaning the data by Trimmomatic and aligning the pair-ends reads by STAR. Please let me know where I am going wrong. I really appreciate your help. My commands:- java -Xmx16G -jar /work/LAS/vollbrec-lab/sharmistha/QoRTs.jar QC --generatePlots --stranded --verbose --maxReadLength 90 --genomeFA /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.fna.gz --rawfastq /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz,/work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz --generateSeparatePlots --outfilePrefix ${output} --chromSizes /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt --addFunctions mismatchEngine,annotatedSpliceExonCounts,FPKM,writeGeneBodyIv,fastqUtils,referenceMatch,writeDocs,makeJunctionBed,makeAllBrowserTracks,calcDetailedGeneCounts /work/LAS/vollbrec-lab/sharmistha/star_files/star_output_files/NB-rep-1_ATCACG_L001/${input1} /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/${output}/ Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017) Starting time: (Mon Jul 02 14:04:41 CDT 2018) INPUT_COMMAND(QC) INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_files/star_output_files/NB-rep-1_ATCACG_L001/NB-rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned/ INPUT_ARG(generatePlots)=true INPUT_ARG(stranded)=true INPUT_ARG(verbose)=true INPUT_ARG(maxReadLength)=Some(90) INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.fna.gz)) INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz)) INPUT_ARG(generateSeparatePlots)=true INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt) INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, makeJunctionBed, makeAllBrowserTracks, calcDetailedGeneCounts) Created Log File: /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.6JZ9kTs4cAFB.log Starting QC [Time: 2018-07-02 14:04:41] [Mem usage: [73MB / 2024MB]] [Elapsed Time: 00:00:00.0000] QoRTs is Running in paired-end mode. QoRTs is Running in any-sorted mode. Chromosome size file added. Adding target wiggle plot generation. Raw fastq files specified. Adding fastq testing. Parameter --genomeFA found. Adding reference mismatch testing. Running functions: CigarOpDistribution, FPKM, GCDistribution, GeneCalcs, InsertSize, JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, annotatedSpliceExonCounts, calcDetailedGeneCounts, chromCounts, cigarLocusCounts, fastqUtils, makeAllBrowserTracks, makeJunctionBed, makeWiggles, mismatchEngine, overlapMatch, readLengthDistro, referenceMatch, writeBiotypeCounts, writeClippedNVC, writeDESeq, writeDEXSeq, writeDocs, writeGeneBody, writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody, Checking first 10000 reads. Checking SAM file for formatting errors... Stats on the first 10000 reads: Num Reads Primary Map: 9103 Num Reads Paired-ended: 10000 Num Reads mapped pair: 9098 Num Pair names found: 4797 Num Pairs matched: 4301 Read Seq length: 36 to 90 Unclipped Read length: 36 to 90 Final maxReadLength: 90 maxPhredScore: 41 minPhredScore: 2 NOTE: Read length is not consistent. In the first 10000 reads, read length varies from 36 to 90 (param maxReadLength=90) Note that using data that is hard-clipped prior to alignment is NOT recommended, because this makes it difficult (or impossible) to determine the sequencer read-cycle of each nucleotide base. This may obfuscate cycle-specific artifacts, trends, or errors, the detection of which is one of the primary purposes of QoRTs!In addition, hard clipping (whether before or after alignment) removes quality score data, and thus quality score metrics may be misleadingly optimistic. A MUCH preferable method of removing undesired sequence is to replace such sequence with N's, which preserves the quality score and the sequencer cycle information. Note: Data appears to be paired-ended. Sorting Note: Reads are not sorted by name (This is OK). Sorting Note: Reads are sorted by position (This is OK). Done checking first 10000 reads. No major problems detected! Starting getSRPairIterResorted... SAMRecord Reader Generated. Read length: 90. [Time: 2018-07-02 14:04:44] [Mem usage: [285MB / 2552MB]] [Elapsed Time: 00:00:03.0401] Starting fastq readthrough. Init FastqGC Utility Init FastqQualityScore Utility Init FastqNVC Utility ============================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.ArrayIndexOutOfBoundsException: 100 at qcUtils.fqcGC.runOnReadPair(fqcGC.scala:43) at qcUtils.runAllQC$.$anonfun$runOnSeqFile$5(runAllQC.scala:1187) at scala.collection.Iterator.foreach(Iterator.scala:929) at scala.collection.Iterator.foreach$(Iterator.scala:929) at scala.collection.AbstractIterator.foreach(Iterator.scala:1417) at scala.collection.IterableLike.foreach(IterableLike.scala:71) at scala.collection.IterableLike.foreach$(IterableLike.scala:70) at scala.collection.AbstractIterable.foreach(Iterable.scala:54) at qcUtils.runAllQC$.$anonfun$runOnSeqFile$4(runAllQC.scala:1187) at qcUtils.runAllQC$.$anonfun$runOnSeqFile$4$adapted(runAllQC.scala:1186) at scala.collection.Iterator.foreach(Iterator.scala:929) at scala.collection.Iterator.foreach$(Iterator.scala:929) at scala.collection.AbstractIterator.foreach(Iterator.scala:1417) at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1186) 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) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#66>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwu7AbkyNWSn_kOPQNs3TdtqYtBCmj-ks5uCnQkgaJpZM4U_0qk> .

[ghost]

Dear Hartleys,
Thank you for your suggestion. It started working when I changed maxreadlength to 100. However, it is giving a different error now.

Thank you for your help.
Sharmistha

Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017)
Starting time: (Thu Jul 05 15:42:34 CDT 2018)
INPUT_COMMAND(QC)
INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_files/star_output_files/coordinate-sorted_BAMfiles/NB-rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam
INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz
INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned/
INPUT_ARG(generatePlots)=true
INPUT_ARG(stranded)=true
INPUT_ARG(verbose)=true
INPUT_ARG(maxReadLength)=Some(100)
INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.fna.gz))
INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz))
INPUT_ARG(generateSeparatePlots)=true
INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned
INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt)
INPUT_ARG(skipFunctions)=List(cigarLocusCounts)
INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, makeJunctionBed, calcDetailedGeneCounts)
Created Log File: /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.bdRqM78mge2M.log
Warning: run-in-progress file "/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.QORTS_RUNNING" already exists. Is there another QoRTs job running?
Starting QC
[Time: 2018-07-05 15:42:34] [Mem usage: [73MB / 2024MB]] [Elapsed Time: 00:00:00.0000]
QoRTs is Running in paired-end mode.
QoRTs is Running in any-sorted mode.
Chromosome size file added. Adding target wiggle plot generation.
Raw fastq files specified. Adding fastq testing.
Parameter --genomeFA found. Adding reference mismatch testing.
Running functions: CigarOpDistribution, FPKM, GCDistribution, GeneCalcs, InsertSize,
JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck,
annotatedSpliceExonCounts, calcDetailedGeneCounts,
chromCounts, fastqUtils, makeJunctionBed, makeWiggles,
mismatchEngine, overlapMatch, readLengthDistro,
referenceMatch, writeBiotypeCounts, writeClippedNVC,
writeDESeq, writeDEXSeq, writeDocs, writeGeneBody,
writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody,
writeJunctionSeqCounts, writeKnownSplices,
writeNovelSplices, writeSpliceExon
Checking first 10000 reads. Checking SAM file for formatting errors...
Stats on the first 10000 reads:
Num Reads Primary Map: 9103
Num Reads Paired-ended: 10000
Num Reads mapped pair: 9098
Num Pair names found: 4797
Num Pairs matched: 4301
Read Seq length: 36 to 90
Unclipped Read length: 36 to 90
Final maxReadLength: 100
maxPhredScore: 41
minPhredScore: 2
NOTE: Read length is not consistent.
In the first 10000 reads, read length varies from 36 to 90 (param maxReadLength=100)

[hartleys]

What error? I dont see any error.

…

On Thu, Jul 5, 2018, 5:28 PM SHARMISTHA CHAKRABORTTY < ***@***.***> wrote: Dear Hartleys, Thank you for your suggestion. It started working when I changed maxreadlength to 100. However, it is giving a different error now. Thank you for your help. Sharmistha Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017) Starting time: (Thu Jul 05 15:42:34 CDT 2018) INPUT_COMMAND(QC) INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_files/star_output_files/coordinate-sorted_BAMfiles/NB-rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned/ INPUT_ARG(generatePlots)=true INPUT_ARG(stranded)=true INPUT_ARG(verbose)=true INPUT_ARG(maxReadLength)=Some(100) INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.fna.gz)) INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz)) INPUT_ARG(generateSeparatePlots)=true INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt) INPUT_ARG(skipFunctions)=List(cigarLocusCounts) INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, makeJunctionBed, calcDetailedGeneCounts) Created Log File: /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.bdRqM78mge2M.log Warning: run-in-progress file "/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep-1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.QORTS_RUNNING" already exists. Is there another QoRTs job running? Starting QC [Time: 2018-07-05 15:42:34] [Mem usage: [73MB / 2024MB]] [Elapsed Time: 00:00:00.0000] QoRTs is Running in paired-end mode. QoRTs is Running in any-sorted mode. Chromosome size file added. Adding target wiggle plot generation. Raw fastq files specified. Adding fastq testing. Parameter --genomeFA found. Adding reference mismatch testing. Running functions: CigarOpDistribution, FPKM, GCDistribution, GeneCalcs, InsertSize, JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, annotatedSpliceExonCounts, calcDetailedGeneCounts, chromCounts, fastqUtils, makeJunctionBed, makeWiggles, mismatchEngine, overlapMatch, readLengthDistro, referenceMatch, writeBiotypeCounts, writeClippedNVC, writeDESeq, writeDEXSeq, writeDocs, writeGeneBody, writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody, writeJunctionSeqCounts, writeKnownSplices, writeNovelSplices, writeSpliceExon Checking first 10000 reads. Checking SAM file for formatting errors... Stats on the first 10000 reads: Num Reads Primary Map: 9103 Num Reads Paired-ended: 10000 Num Reads mapped pair: 9098 Num Pair names found: 4797 Num Pairs matched: 4301 Read Seq length: 36 to 90 Unclipped Read length: 36 to 90 Final maxReadLength: 100 maxPhredScore: 41 minPhredScore: 2 NOTE: Read length is not consistent. In the first 10000 reads, read length varies from 36 to 90 (param maxReadLength=100) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#66 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwu7GKvLL1qaiKre1Tqp6tlL6Rp3iYjks5uDoTlgaJpZM4U_0qk> .

[ghost]

Dear Hartley, Sorry I missed pasting the error. This is the error I am getting. Finished fastq readthrough.

Init GeneCalcs Utility Init InsertSize Utility

Compiling flat feature annotation, internally in memory... FlatteningGtf: starting...(2018-07-05 16:07:17) FlatteningGtf: gtf file read complete.(2018-07-05 16:07:35) FlatteningGtf: Splice Junction Map read.(2018-07-05 16:07:37) FlatteningGtf: gene Sets generated.(2018-07-05 16:07:38) FlatteningGtf: Aggregate Sets built. FlatteningGtf: Compiling Aggregate Info . . . (2018-07-05 16:07:38) FlatteningGtf: Finished Compiling Aggregate Info. (2018-07-05 16:07:38) FlatteningGtf: Iterating through the step-vector...(2018-07-05 16:07:38) FlatteningGtf: Adding the aggregate genes themselves...(2018-07-05 16:07:40) FlatteningGtf: Iterating through the splice junctions...(2018-07-05 16:07:40) FlatteningGtf: Sorting the aggregate genes...(2018-07-05 16:07:41) FlatteningGtf: Folding the FlatGtfLine iterator...(2018-07-05 16:07:41) FlatteningGtf: Features Built.(2018-07-05 16:07:41) Internal flat feature annotation compiled!

Init NVC utility Init CigarOpDistribution Utility Init QualityScoreDistribution Utility Init GC counts Utility Init JunctionCalcs utility

length of knownSpliceMap after instantiation: 244072 length of knownCountMap after instantiation: 244072

Init StrandCheck Utility Init chromCount Utility

Beginning allocation of genomic window array... ============================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.ArrayIndexOutOfBoundsException: 1 at fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1(bamToWiggle.scala:774) at fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1$adapted(bamToWiggle.scala:771) at scala.collection.Iterator.foreach(Iterator.scala:929) at scala.collection.Iterator.foreach$(Iterator.scala:929) at scala.collection.AbstractIterator.foreach(Iterator.scala:1417) at fileConversionUtils.bamToWiggle$.genChrom(bamToWiggle.scala:771) at fileConversionUtils.bamToWiggle$QcBamToWig.<init>(bamToWiggle.scala:618) at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1225) 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) Thanks for your help, Sharmistha On Thu, Jul 5, 2018 at 11:33 PM, Steve Hartley <notifications@github.com> wrote:

…

What error? I dont see any error. On Thu, Jul 5, 2018, 5:28 PM SHARMISTHA CHAKRABORTTY < ***@***.***> wrote: > Dear Hartleys, > Thank you for your suggestion. It started working when I changed > maxreadlength to 100. However, it is giving a different error now. > > Thank you for your help. > Sharmistha > > Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017) > Starting time: (Thu Jul 05 15:42:34 CDT 2018) > INPUT_COMMAND(QC) > > INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_ files/star_output_files/coordinate-sorted_BAMfiles/NB- rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam > > INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_ files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz > > INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_ files/NB-rep-1_ATCACG_L001Aligned/ > INPUT_ARG(generatePlots)=true > INPUT_ARG(stranded)=true > INPUT_ARG(verbose)=true > INPUT_ARG(maxReadLength)=Some(100) > > INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/ sharmistha/star_files/GenomeFiles/GCA_000005005.6_ B73_RefGen_v4_genomic.fna.gz)) > INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/ sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, > /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz)) > INPUT_ARG(generateSeparatePlots)=true > INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned > > INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/ GenomeDirectory/chrLength.txt) > INPUT_ARG(skipFunctions)=List(cigarLocusCounts) > INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, > FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, > makeJunctionBed, calcDetailedGeneCounts) > Created Log File: > /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.bdRqM78mge2M.log > Warning: run-in-progress file > "/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.QORTS_RUNNING" > already exists. Is there another QoRTs job running? > Starting QC > [Time: 2018-07-05 15:42:34] [Mem usage: [73MB / 2024MB]] [Elapsed Time: > 00:00:00.0000] > QoRTs is Running in paired-end mode. > QoRTs is Running in any-sorted mode. > Chromosome size file added. Adding target wiggle plot generation. > Raw fastq files specified. Adding fastq testing. > Parameter --genomeFA found. Adding reference mismatch testing. > Running functions: CigarOpDistribution, FPKM, GCDistribution, GeneCalcs, > InsertSize, > JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, > annotatedSpliceExonCounts, calcDetailedGeneCounts, > chromCounts, fastqUtils, makeJunctionBed, makeWiggles, > mismatchEngine, overlapMatch, readLengthDistro, > referenceMatch, writeBiotypeCounts, writeClippedNVC, > writeDESeq, writeDEXSeq, writeDocs, writeGeneBody, > writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody, > writeJunctionSeqCounts, writeKnownSplices, > writeNovelSplices, writeSpliceExon > Checking first 10000 reads. Checking SAM file for formatting errors... > Stats on the first 10000 reads: > Num Reads Primary Map: 9103 > Num Reads Paired-ended: 10000 > Num Reads mapped pair: 9098 > Num Pair names found: 4797 > Num Pairs matched: 4301 > Read Seq length: 36 to 90 > Unclipped Read length: 36 to 90 > Final maxReadLength: 100 > maxPhredScore: 41 > minPhredScore: 2 > NOTE: Read length is not consistent. > In the first 10000 reads, read length varies from 36 to 90 (param > maxReadLength=100) > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#66 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ ACwu7GKvLL1qaiKre1Tqp6tlL6Rp3iYjks5uDoTlgaJpZM4U_0qk> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#66 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHhVms8UH8rCQ7q2O0iW5QiQJJwOi90jks5uDuiagaJpZM4U_0qk> .

[hartleys]

Can I see the chrome length file? Aka /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt On Fri, Jul 6, 2018, 11:18 AM SHARMISTHA CHAKRABORTTY < notifications@github.com> wrote:

…

Dear Hartley, Sorry I missed pasting the error. This is the error I am getting. Finished fastq readthrough. > Init GeneCalcs Utility > Init InsertSize Utility Compiling flat feature annotation, internally in memory... FlatteningGtf: starting...(2018-07-05 16:07:17) FlatteningGtf: gtf file read complete.(2018-07-05 16:07:35) FlatteningGtf: Splice Junction Map read.(2018-07-05 16:07:37) FlatteningGtf: gene Sets generated.(2018-07-05 16:07:38) FlatteningGtf: Aggregate Sets built. FlatteningGtf: Compiling Aggregate Info . . . (2018-07-05 16:07:38) FlatteningGtf: Finished Compiling Aggregate Info. (2018-07-05 16:07:38) FlatteningGtf: Iterating through the step-vector...(2018-07-05 16:07:38) FlatteningGtf: Adding the aggregate genes themselves...(2018-07-05 16:07:40) FlatteningGtf: Iterating through the splice junctions...(2018-07-05 16:07:40) FlatteningGtf: Sorting the aggregate genes...(2018-07-05 16:07:41) FlatteningGtf: Folding the FlatGtfLine iterator...(2018-07-05 16:07:41) FlatteningGtf: Features Built.(2018-07-05 16:07:41) Internal flat feature annotation compiled! > Init NVC utility > Init CigarOpDistribution Utility > Init QualityScoreDistribution Utility > Init GC counts Utility > Init JunctionCalcs utility length of knownSpliceMap after instantiation: 244072 length of knownCountMap after instantiation: 244072 > Init StrandCheck Utility > Init chromCount Utility Beginning allocation of genomic window array... ============================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.ArrayIndexOutOfBoundsException: 1 at fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1(bamToWiggle.scala:774) at fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1$adapted(bamToWiggle.scala:771) at scala.collection.Iterator.foreach(Iterator.scala:929) at scala.collection.Iterator.foreach$(Iterator.scala:929) at scala.collection.AbstractIterator.foreach(Iterator.scala:1417) at fileConversionUtils.bamToWiggle$.genChrom(bamToWiggle.scala:771) at fileConversionUtils.bamToWiggle$QcBamToWig.<init>(bamToWiggle.scala:618) at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1225) 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) Thanks for your help, Sharmistha On Thu, Jul 5, 2018 at 11:33 PM, Steve Hartley ***@***.***> wrote: > What error? I dont see any error. > > On Thu, Jul 5, 2018, 5:28 PM SHARMISTHA CHAKRABORTTY < > ***@***.***> wrote: > > > Dear Hartleys, > > Thank you for your suggestion. It started working when I changed > > maxreadlength to 100. However, it is giving a different error now. > > > > Thank you for your help. > > Sharmistha > > > > Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017) > > Starting time: (Thu Jul 05 15:42:34 CDT 2018) > > INPUT_COMMAND(QC) > > > > INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_ > files/star_output_files/coordinate-sorted_BAMfiles/NB- > rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam > > > > INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_ > files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz > > > > INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_ > files/NB-rep-1_ATCACG_L001Aligned/ > > INPUT_ARG(generatePlots)=true > > INPUT_ARG(stranded)=true > > INPUT_ARG(verbose)=true > > INPUT_ARG(maxReadLength)=Some(100) > > > > INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/ > sharmistha/star_files/GenomeFiles/GCA_000005005.6_ > B73_RefGen_v4_genomic.fna.gz)) > > INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/ > sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, > > /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz)) > > INPUT_ARG(generateSeparatePlots)=true > > INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned > > > > INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/ > GenomeDirectory/chrLength.txt) > > INPUT_ARG(skipFunctions)=List(cigarLocusCounts) > > INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, > > FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, > > makeJunctionBed, calcDetailedGeneCounts) > > Created Log File: > > /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- > 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.bdRqM78mge2M.log > > Warning: run-in-progress file > > "/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- > 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.QORTS_RUNNING" > > already exists. Is there another QoRTs job running? > > Starting QC > > [Time: 2018-07-05 15:42:34] [Mem usage: [73MB / 2024MB]] [Elapsed Time: > > 00:00:00.0000] > > QoRTs is Running in paired-end mode. > > QoRTs is Running in any-sorted mode. > > Chromosome size file added. Adding target wiggle plot generation. > > Raw fastq files specified. Adding fastq testing. > > Parameter --genomeFA found. Adding reference mismatch testing. > > Running functions: CigarOpDistribution, FPKM, GCDistribution, GeneCalcs, > > InsertSize, > > JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, > > annotatedSpliceExonCounts, calcDetailedGeneCounts, > > chromCounts, fastqUtils, makeJunctionBed, makeWiggles, > > mismatchEngine, overlapMatch, readLengthDistro, > > referenceMatch, writeBiotypeCounts, writeClippedNVC, > > writeDESeq, writeDEXSeq, writeDocs, writeGeneBody, > > writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody, > > writeJunctionSeqCounts, writeKnownSplices, > > writeNovelSplices, writeSpliceExon > > Checking first 10000 reads. Checking SAM file for formatting errors... > > Stats on the first 10000 reads: > > Num Reads Primary Map: 9103 > > Num Reads Paired-ended: 10000 > > Num Reads mapped pair: 9098 > > Num Pair names found: 4797 > > Num Pairs matched: 4301 > > Read Seq length: 36 to 90 > > Unclipped Read length: 36 to 90 > > Final maxReadLength: 100 > > maxPhredScore: 41 > > minPhredScore: 2 > > NOTE: Read length is not consistent. > > In the first 10000 reads, read length varies from 36 to 90 (param > > maxReadLength=100) > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#66 (comment)>, > or mute > > the thread > > <https://github.com/notifications/unsubscribe-auth/ > ACwu7GKvLL1qaiKre1Tqp6tlL6Rp3iYjks5uDoTlgaJpZM4U_0qk> > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#66 (comment)>, or mute > the thread > < https://github.com/notifications/unsubscribe-auth/AHhVms8UH8rCQ7q2O0iW5QiQJJwOi90jks5uDuiagaJpZM4U_0qk > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#66 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwu7PIy3B4t2Xk8uxO29oN5u1TBiXS3ks5uD3_DgaJpZM4U_0qk> .

[ghost]

Dear Hartley, Please find the attached chromosome length txt file. Sharmistha On Fri, Jul 6, 2018 at 12:19 PM, Steve Hartley <notifications@github.com> wrote:

Can I see the chrome length file? Aka /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt On Fri, Jul 6, 2018, 11:18 AM SHARMISTHA CHAKRABORTTY < ***@***.***> wrote: > Dear Hartley, > > Sorry I missed pasting the error. This is the error I am getting. > > > Finished fastq readthrough. > > Init GeneCalcs Utility > > Init InsertSize Utility > Compiling flat feature annotation, internally in memory... > FlatteningGtf: starting...(2018-07-05 16:07:17) > FlatteningGtf: gtf file read complete.(2018-07-05 16:07:35) > FlatteningGtf: Splice Junction Map read.(2018-07-05 16:07:37) > FlatteningGtf: gene Sets generated.(2018-07-05 16:07:38) > FlatteningGtf: Aggregate Sets built. > FlatteningGtf: Compiling Aggregate Info . . . (2018-07-05 16:07:38) > FlatteningGtf: Finished Compiling Aggregate Info. (2018-07-05 16:07:38) > FlatteningGtf: Iterating through the step-vector...(2018-07-05 16:07:38) > FlatteningGtf: Adding the aggregate genes themselves...(2018-07-05 > 16:07:40) > FlatteningGtf: Iterating through the splice junctions...(2018-07-05 > 16:07:40) > FlatteningGtf: Sorting the aggregate genes...(2018-07-05 16:07:41) > FlatteningGtf: Folding the FlatGtfLine iterator...(2018-07-05 16:07:41) > FlatteningGtf: Features Built.(2018-07-05 16:07:41) > Internal flat feature annotation compiled! > > Init NVC utility > > Init CigarOpDistribution Utility > > Init QualityScoreDistribution Utility > > Init GC counts Utility > > Init JunctionCalcs utility > length of knownSpliceMap after instantiation: 244072 > length of knownCountMap after instantiation: 244072 > > Init StrandCheck Utility > > Init chromCount Utility > Beginning allocation of genomic window array... > ============================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.ArrayIndexOutOfBoundsException: 1 > at > fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1(bamToWiggle.scala: 774) > at > > fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1$adapted( bamToWiggle.scala:771) > at scala.collection.Iterator.foreach(Iterator.scala:929) > at scala.collection.Iterator.foreach$(Iterator.scala:929) > at scala.collection.AbstractIterator.foreach(Iterator.scala:1417) > at fileConversionUtils.bamToWiggle$.genChrom(bamToWiggle.scala:771) > at > fileConversionUtils.bamToWiggle$QcBamToWig.<init>(bamToWiggle.scala:618) > at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1225) > 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) > > > Thanks for your help, > Sharmistha > > > On Thu, Jul 5, 2018 at 11:33 PM, Steve Hartley ***@***.*** > > wrote: > > > What error? I dont see any error. > > > > On Thu, Jul 5, 2018, 5:28 PM SHARMISTHA CHAKRABORTTY < > > ***@***.***> wrote: > > > > > Dear Hartleys, > > > Thank you for your suggestion. It started working when I changed > > > maxreadlength to 100. However, it is giving a different error now. > > > > > > Thank you for your help. > > > Sharmistha > > > > > > Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017) > > > Starting time: (Thu Jul 05 15:42:34 CDT 2018) > > > INPUT_COMMAND(QC) > > > > > > INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_ > > files/star_output_files/coordinate-sorted_BAMfiles/NB- > > rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam > > > > > > INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_ > > files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz > > > > > > INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_ > > files/NB-rep-1_ATCACG_L001Aligned/ > > > INPUT_ARG(generatePlots)=true > > > INPUT_ARG(stranded)=true > > > INPUT_ARG(verbose)=true > > > INPUT_ARG(maxReadLength)=Some(100) > > > > > > INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/ > > sharmistha/star_files/GenomeFiles/GCA_000005005.6_ > > B73_RefGen_v4_genomic.fna.gz)) > > > INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/ > > sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, > > > > /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz)) > > > INPUT_ARG(generateSeparatePlots)=true > > > INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned > > > > > > > INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/ > > GenomeDirectory/chrLength.txt) > > > INPUT_ARG(skipFunctions)=List(cigarLocusCounts) > > > INPUT_ARG(addFunctions)=List(mismatchEngine, annotatedSpliceExonCounts, > > > FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, > > > makeJunctionBed, calcDetailedGeneCounts) > > > Created Log File: > > > /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- > > 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.bdRqM78mge2M.log > > > Warning: run-in-progress file > > > "/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- > > 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.QORTS_RUNNING" > > > already exists. Is there another QoRTs job running? > > > Starting QC > > > [Time: 2018-07-05 15:42:34] [Mem usage: [73MB / 2024MB]] [Elapsed Time: > > > 00:00:00.0000] > > > QoRTs is Running in paired-end mode. > > > QoRTs is Running in any-sorted mode. > > > Chromosome size file added. Adding target wiggle plot generation. > > > Raw fastq files specified. Adding fastq testing. > > > Parameter --genomeFA found. Adding reference mismatch testing. > > > Running functions: CigarOpDistribution, FPKM, GCDistribution, > GeneCalcs, > > > InsertSize, > > > JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, > > > annotatedSpliceExonCounts, calcDetailedGeneCounts, > > > chromCounts, fastqUtils, makeJunctionBed, makeWiggles, > > > mismatchEngine, overlapMatch, readLengthDistro, > > > referenceMatch, writeBiotypeCounts, writeClippedNVC, > > > writeDESeq, writeDEXSeq, writeDocs, writeGeneBody, > > > writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody, > > > writeJunctionSeqCounts, writeKnownSplices, > > > writeNovelSplices, writeSpliceExon > > > Checking first 10000 reads. Checking SAM file for formatting errors... > > > Stats on the first 10000 reads: > > > Num Reads Primary Map: 9103 > > > Num Reads Paired-ended: 10000 > > > Num Reads mapped pair: 9098 > > > Num Pair names found: 4797 > > > Num Pairs matched: 4301 > > > Read Seq length: 36 to 90 > > > Unclipped Read length: 36 to 90 > > > Final maxReadLength: 100 > > > maxPhredScore: 41 > > > minPhredScore: 2 > > > NOTE: Read length is not consistent. > > > In the first 10000 reads, read length varies from 36 to 90 (param > > > maxReadLength=100) > > > > > > — > > > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > > > <#66 (comment) >, > > or mute > > > the thread > > > <https://github.com/notifications/unsubscribe-auth/ > > ACwu7GKvLL1qaiKre1Tqp6tlL6Rp3iYjks5uDoTlgaJpZM4U_0qk> > > > > > . > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#66 (comment)>, > or mute > > the thread > > < > https://github.com/notifications/unsubscribe-auth/ AHhVms8UH8rCQ7q2O0iW5QiQJJwOi90jks5uDuiagaJpZM4U_0qk > > > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#66 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ ACwu7PIy3B4t2Xk8uxO29oN5u1TBiXS3ks5uD3_DgaJpZM4U_0qk> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#66 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHhVmr_Ht2kb4OBysC81rSdGFs2eWCmFks5uD5wOgaJpZM4U_0qk> .

307041717 244442276 235667834 246994605 223902240 174033170 182381542 181122637 159769782 150982314 50531 60109 59657 66261 83265 255484 71433 64470 110418 992858 100537 34930 70946 84781 55297 94873 70750 70926 76840 89036 65749 24080 77423 70597 41524 215635 11339 65819 66393 110255 846561 54684 108212 39815 74491 70486 48545 91381 29460 84148 66656 67687 45711 101180 57348 65659 33120 72581 100579 381258 83120 756422 458256 82446 695048 62662 65407 53907 117437 76354 92234 63530 51910 666287 69959 60926 60205 65268 54868 77242 342161 83778 81536 516616 5568 87707 93364 73283 65470 80451 83476 67579 98601 109991 47381 57632 58721 82793 52427 795190 94431 58809 55397 76262 44176 90109 103641 36676 87733 76596 101603 83681 85134 61773 57130 83503 57822 134067 57973 107933 139473 62853 67958 71809 9476 79679 62538 43926 55817 63567 90796 95420 44508 79882 9160 46935 86301 254428 73561 40576 83845 83688 86441 57064 60070 78370 40594 56161 344981 63556 739442 51967 53538 66893 69976 70601 73006 58809 1738914 63917 69060 65477 58645 128268 60365 55665 48311 77382 31799 50526 40634 50620 66428 67904 59352 53643 54946 47089 105189 72536 43047 66538 66228 69465 59418 41679 340736 85784 80324 351693 1278389 96695 52129 56966 64245 6454 82080 71282 59524 72401 66116 526805 41461 58299 138544 45447 46041 60303 54466 73251 53313 82450 28410 55164 73968 46344 67134 58608 60995 55641 43787 74799 74080 55962 61539 58830 53522 61449 62284 44889 80070 63290 55301 64997 53614 41417 17651 85258 65674 73141 52477 94458 36081 70135 54117 7104 61153 95256 45166 52360 56713 51365 48860 76559 47028 81363 66018 30460 63031 51883 52549 82972 69595 46945 124116

[hartleys]

I dont understand what format this is. The chrome length file needs to be two tab delimited columns: chromosome name and then chromosome length. What species / ref genome is this? On Fri, Jul 6, 2018, 3:02 PM SHARMISTHA CHAKRABORTTY < notifications@github.com> wrote:

…

Dear Hartley, Please find the attached chromosome length txt file. Sharmistha On Fri, Jul 6, 2018 at 12:19 PM, Steve Hartley ***@***.***> wrote: > Can I see the chrome length file? > > Aka > /work/LAS/vollbrec-lab/sharmistha/star_files/GenomeDirectory/chrLength.txt > > On Fri, Jul 6, 2018, 11:18 AM SHARMISTHA CHAKRABORTTY < > > ***@***.***> wrote: > > > Dear Hartley, > > > > Sorry I missed pasting the error. This is the error I am getting. > > > > > > Finished fastq readthrough. > > > Init GeneCalcs Utility > > > Init InsertSize Utility > > Compiling flat feature annotation, internally in memory... > > FlatteningGtf: starting...(2018-07-05 16:07:17) > > FlatteningGtf: gtf file read complete.(2018-07-05 16:07:35) > > FlatteningGtf: Splice Junction Map read.(2018-07-05 16:07:37) > > FlatteningGtf: gene Sets generated.(2018-07-05 16:07:38) > > FlatteningGtf: Aggregate Sets built. > > FlatteningGtf: Compiling Aggregate Info . . . (2018-07-05 16:07:38) > > FlatteningGtf: Finished Compiling Aggregate Info. (2018-07-05 16:07:38) > > FlatteningGtf: Iterating through the step-vector...(2018-07-05 16:07:38) > > FlatteningGtf: Adding the aggregate genes themselves...(2018-07-05 > > 16:07:40) > > FlatteningGtf: Iterating through the splice junctions...(2018-07-05 > > 16:07:40) > > FlatteningGtf: Sorting the aggregate genes...(2018-07-05 16:07:41) > > FlatteningGtf: Folding the FlatGtfLine iterator...(2018-07-05 16:07:41) > > FlatteningGtf: Features Built.(2018-07-05 16:07:41) > > Internal flat feature annotation compiled! > > > Init NVC utility > > > Init CigarOpDistribution Utility > > > Init QualityScoreDistribution Utility > > > Init GC counts Utility > > > Init JunctionCalcs utility > > length of knownSpliceMap after instantiation: 244072 > > length of knownCountMap after instantiation: 244072 > > > Init StrandCheck Utility > > > Init chromCount Utility > > Beginning allocation of genomic window array... > > ============================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.ArrayIndexOutOfBoundsException: 1 > > at > > fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1(bamToWiggle.scala: > 774) > > at > > > > fileConversionUtils.bamToWiggle$.$anonfun$genChrom$1$adapted( > bamToWiggle.scala:771) > > at scala.collection.Iterator.foreach(Iterator.scala:929) > > at scala.collection.Iterator.foreach$(Iterator.scala:929) > > at scala.collection.AbstractIterator.foreach(Iterator.scala:1417) > > at fileConversionUtils.bamToWiggle$.genChrom(bamToWiggle.scala:771) > > at > > fileConversionUtils.bamToWiggle$QcBamToWig.<init>(bamToWiggle.scala:618) > > at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1225) > > 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) > > > > > > Thanks for your help, > > Sharmistha > > > > > > On Thu, Jul 5, 2018 at 11:33 PM, Steve Hartley < ***@***.*** > > > > wrote: > > > > > What error? I dont see any error. > > > > > > On Thu, Jul 5, 2018, 5:28 PM SHARMISTHA CHAKRABORTTY < > > > ***@***.***> wrote: > > > > > > > Dear Hartleys, > > > > Thank you for your suggestion. It started working when I changed > > > > maxreadlength to 100. However, it is giving a different error now. > > > > > > > > Thank you for your help. > > > > Sharmistha > > > > > > > > Starting QoRTs v1.3.0 (Compiled Fri Oct 20 11:56:37 EDT 2017) > > > > Starting time: (Thu Jul 05 15:42:34 CDT 2018) > > > > INPUT_COMMAND(QC) > > > > > > > > INPUT_ARG(infile)=/work/LAS/vollbrec-lab/sharmistha/star_ > > > files/star_output_files/coordinate-sorted_BAMfiles/NB- > > > rep-1_ATCACG_L001Aligned.sortedByCoord.out.bam > > > > > > > > INPUT_ARG(gtffile)=/work/LAS/vollbrec-lab/sharmistha/star_ > > > files/GenomeFiles/GCA_000005005.6_B73_RefGen_v4_genomic.gtf.gz > > > > > > > > INPUT_ARG(outdir)=/work/LAS/vollbrec-lab/sharmistha/QoRTs_ > > > files/NB-rep-1_ATCACG_L001Aligned/ > > > > INPUT_ARG(generatePlots)=true > > > > INPUT_ARG(stranded)=true > > > > INPUT_ARG(verbose)=true > > > > INPUT_ARG(maxReadLength)=Some(100) > > > > > > > > INPUT_ARG(genomeFA)=Some(List(/work/LAS/vollbrec-lab/ > > > sharmistha/star_files/GenomeFiles/GCA_000005005.6_ > > > B73_RefGen_v4_genomic.fna.gz)) > > > > INPUT_ARG(rawfastq)=Some(List(/work/LAS/vollbrec-lab/ > > > sharmistha/NB-rep-1_ATCACG_L001_R1_001.fastq.gz, > > > > > > /work/LAS/vollbrec-lab/sharmistha/NB-rep-1_ATCACG_L001_R2_001.fastq.gz)) > > > > INPUT_ARG(generateSeparatePlots)=true > > > > INPUT_ARG(outfilePrefix)=NB-rep-1_ATCACG_L001Aligned > > > > > > > > > > INPUT_ARG(chromSizes)=Some(/work/LAS/vollbrec-lab/sharmistha/star_files/ > > > GenomeDirectory/chrLength.txt) > > > > INPUT_ARG(skipFunctions)=List(cigarLocusCounts) > > > > INPUT_ARG(addFunctions)=List(mismatchEngine, > annotatedSpliceExonCounts, > > > > FPKM, writeGeneBodyIv, fastqUtils, referenceMatch, writeDocs, > > > > makeJunctionBed, calcDetailedGeneCounts) > > > > Created Log File: > > > > /work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- > > > 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.bdRqM78mge2M.log > > > > Warning: run-in-progress file > > > > "/work/LAS/vollbrec-lab/sharmistha/QoRTs_files/NB-rep- > > > 1_ATCACG_L001Aligned//NB-rep-1_ATCACG_L001AlignedQC.QORTS_RUNNING" > > > > already exists. Is there another QoRTs job running? > > > > Starting QC > > > > [Time: 2018-07-05 15:42:34] [Mem usage: [73MB / 2024MB]] [Elapsed > Time: > > > > 00:00:00.0000] > > > > QoRTs is Running in paired-end mode. > > > > QoRTs is Running in any-sorted mode. > > > > Chromosome size file added. Adding target wiggle plot generation. > > > > Raw fastq files specified. Adding fastq testing. > > > > Parameter --genomeFA found. Adding reference mismatch testing. > > > > Running functions: CigarOpDistribution, FPKM, GCDistribution, > > GeneCalcs, > > > > InsertSize, > > > > JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, > > > > annotatedSpliceExonCounts, calcDetailedGeneCounts, > > > > chromCounts, fastqUtils, makeJunctionBed, makeWiggles, > > > > mismatchEngine, overlapMatch, readLengthDistro, > > > > referenceMatch, writeBiotypeCounts, writeClippedNVC, > > > > writeDESeq, writeDEXSeq, writeDocs, writeGeneBody, > > > > writeGeneBodyIv, writeGeneCounts, writeGenewiseGeneBody, > > > > writeJunctionSeqCounts, writeKnownSplices, > > > > writeNovelSplices, writeSpliceExon > > > > Checking first 10000 reads. Checking SAM file for formatting > errors... > > > > Stats on the first 10000 reads: > > > > Num Reads Primary Map: 9103 > > > > Num Reads Paired-ended: 10000 > > > > Num Reads mapped pair: 9098 > > > > Num Pair names found: 4797 > > > > Num Pairs matched: 4301 > > > > Read Seq length: 36 to 90 > > > > Unclipped Read length: 36 to 90 > > > > Final maxReadLength: 100 > > > > maxPhredScore: 41 > > > > minPhredScore: 2 > > > > NOTE: Read length is not consistent. > > > > In the first 10000 reads, read length varies from 36 to 90 (param > > > > maxReadLength=100) > > > > > > > > — > > > > You are receiving this because you commented. > > > > Reply to this email directly, view it on GitHub > > > > < #66 (comment) > >, > > > or mute > > > > the thread > > > > <https://github.com/notifications/unsubscribe-auth/ > > > ACwu7GKvLL1qaiKre1Tqp6tlL6Rp3iYjks5uDoTlgaJpZM4U_0qk> > > > > > > > . > > > > > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > <#66 (comment) >, > > or mute > > > the thread > > > < > > https://github.com/notifications/unsubscribe-auth/ > AHhVms8UH8rCQ7q2O0iW5QiQJJwOi90jks5uDuiagaJpZM4U_0qk > > > > > > . > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#66 (comment)>, > or mute > > the thread > > <https://github.com/notifications/unsubscribe-auth/ > ACwu7PIy3B4t2Xk8uxO29oN5u1TBiXS3ks5uD3_DgaJpZM4U_0qk> > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#66 (comment)>, or mute > the thread > < https://github.com/notifications/unsubscribe-auth/AHhVmr_Ht2kb4OBysC81rSdGFs2eWCmFks5uD5wOgaJpZM4U_0qk > > . > 307041717 244442276 235667834 246994605 223902240 174033170 182381542 181122637 159769782 150982314 50531 60109 59657 66261 83265 255484 71433 64470 110418 992858 100537 34930 70946 84781 55297 94873 70750 70926 76840 89036 65749 24080 77423 70597 41524 215635 11339 65819 66393 110255 846561 54684 108212 39815 74491 70486 48545 91381 29460 84148 66656 67687 45711 101180 57348 65659 33120 72581 100579 381258 83120 756422 458256 82446 695048 62662 65407 53907 117437 76354 92234 63530 51910 666287 69959 60926 60205 65268 54868 77242 342161 83778 81536 516616 5568 87707 93364 73283 65470 80451 83476 67579 98601 109991 47381 57632 58721 82793 52427 795190 94431 58809 55397 76262 44176 90109 103641 36676 87733 76596 101603 83681 85134 61773 57130 83503 57822 134067 57973 107933 139473 62853 67958 71809 9476 79679 62538 43926 55817 63567 90796 95420 44508 79882 9160 46935 86301 254428 73561 40576 83845 83688 86441 57064 60070 78370 40594 56161 344981 63556 739442 51967 53538 66893 69976 70601 73006 58809 1738914 63917 69060 65477 58645 128268 60365 55665 48311 77382 31799 50526 40634 50620 66428 67904 59352 53643 54946 47089 105189 72536 43047 66538 66228 69465 59418 41679 340736 85784 80324 351693 1278389 96695 52129 56966 64245 6454 82080 71282 59524 72401 66116 526805 41461 58299 138544 45447 46041 60303 54466 73251 53313 82450 28410 55164 73968 46344 67134 58608 60995 55641 43787 74799 74080 55962 61539 58830 53522 61449 62284 44889 80070 63290 55301 64997 53614 41417 17651 85258 65674 73141 52477 94458 36081 70135 54117 7104 61153 95256 45166 52360 56713 51365 48860 76559 47028 81363 66018 30460 63031 51883 52549 82972 69595 46945 124116 — You are receiving this because you commented. 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