Hi,
I used following 4 steps to get sequencing statistics from RNASeqC but I get error, could anyone help me understand and get rid of this error?
Thanks.
RNA-SeQC v1.1.7 05/14/12
Creating rRNA Interval List based on given GTF annotations
java.lang.ArrayIndexOutOfBoundsException: 1
at org.broadinstitute.cga.rnaseq.RNASeqMetrics$MetricSample.readInSamples(RNASeqMetrics.java:1369)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:182)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:165)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:135)
RNA-SeQC Total Runtime: 0 min
-----------------
java -jar picard-tools/v1.87/AddOrReplaceReadGroups.jar I=MCF7/accepted_hits.bam O=MCF7/accepted_hits_readgrps.bam VALIDATION_STRINGENCY=LENIENT SORT_ORDER=coordinate RGID=MCF7 RGCN=MCF7 RGLB=lane6 RGPL=illumina RGPU=lane6 RGSM=accepted_hits.bam
java -jar picard-tools/v1.87/SortSam.jar I=MCF7/accepted_hits_readgrps.bam O=MCF7/accepted_hits_readgrps_sorted.bam SO=coordinate
java -jar picard-tools/v1.87/ReorderSam.jar I=MCF7/accepted_hits_readgrps_sorted.bam O=MCF7/accepted_hits_readgrps_sorted.reordered.bam R=refGenome/hg19.fa CREATE_INDEX=true
java -jar softwares/RNA-SeQC_v1.1.7.jar -n 1000 -s MCF7/accepted_hits_readgrps_sorted.reordered.bam -t index/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2012-03-09-03-24-41/Genes/genes.gtf -r refGenome/hg19.fa -o reportMCF7
I used following 4 steps to get sequencing statistics from RNASeqC but I get error, could anyone help me understand and get rid of this error?
Thanks.
RNA-SeQC v1.1.7 05/14/12
Creating rRNA Interval List based on given GTF annotations
java.lang.ArrayIndexOutOfBoundsException: 1
at org.broadinstitute.cga.rnaseq.RNASeqMetrics$MetricSample.readInSamples(RNASeqMetrics.java:1369)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:182)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:165)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:135)
RNA-SeQC Total Runtime: 0 min
-----------------
java -jar picard-tools/v1.87/AddOrReplaceReadGroups.jar I=MCF7/accepted_hits.bam O=MCF7/accepted_hits_readgrps.bam VALIDATION_STRINGENCY=LENIENT SORT_ORDER=coordinate RGID=MCF7 RGCN=MCF7 RGLB=lane6 RGPL=illumina RGPU=lane6 RGSM=accepted_hits.bam
java -jar picard-tools/v1.87/SortSam.jar I=MCF7/accepted_hits_readgrps.bam O=MCF7/accepted_hits_readgrps_sorted.bam SO=coordinate
java -jar picard-tools/v1.87/ReorderSam.jar I=MCF7/accepted_hits_readgrps_sorted.bam O=MCF7/accepted_hits_readgrps_sorted.reordered.bam R=refGenome/hg19.fa CREATE_INDEX=true
java -jar softwares/RNA-SeQC_v1.1.7.jar -n 1000 -s MCF7/accepted_hits_readgrps_sorted.reordered.bam -t index/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2012-03-09-03-24-41/Genes/genes.gtf -r refGenome/hg19.fa -o reportMCF7
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