Map RNA reads to Transcriptome Assembly

bio@ticuna:/data/process/Roya/mapReadsTransToTranscriptome$ clc_ref_assemble_long -d ../RawDataRoya/RNASeqBGI/Results/Paired_Assemby/Hv701_Trans.fasta -q ../RawDataRoya/RNASeqBGI/Hv701_L1_1.fq ../RawDataRoya/RNASeqBGI/Hv701_L1_2.fq -o mapReadsTransToTranscriptome.cas

Convert cas file to bam file

castosam -a mapReadsTransToTranscriptome.cas -o mapReadsTransToTranscriptome.cas.bam

Sort bam file to generate the index file

samtools sort mapReadsTransToTranscriptome.cas.bam mapReadsTransToTranscriptome.cas.bam.sorted

samtools index mapReadsTransToTranscriptome.cas.bam.sorted.bam

Generate .sam to generate .gtf

/opt/cufflinks-1.3.0.Linux_x86_64/cufflinks mapReadsTransToTranscriptome.cas.sorted.bam

Executing RNA-SeQC

bio@ticuna:/data/process/Roya/mapReadsTransToTranscriptome$ java -jar /opt/RNA-SeQC/RNA-SeQC_v1.0.1.jar -n 1000 -s “TestId|mapReadsTransToTranscriptome.cas.bam.sorted.bam|TestDesc” -t transcripts.gtf -r Hv701_Trans.fasta -o ./testReport

Creating rRNA Interval List based on given GTF annotations
Retriving contig names from reference
         contig names in reference: 55791
Loading GTF for Read Counting
Converting to refGene
Transcript objects to RefGen format:    531 s
java.lang.RuntimeException: No rRNA found in GTF transcript_type field
        at org.broadinstitute.cga.rnaseq.TranscriptList.toRRNAIntervalList(TranscriptList.java:329)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.createRefGeneAndRRNAFiles(RNASeqMetrics.java:955)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:164)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:141)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:116)
RNASeqMetrics Total Runtime:    8 min

Error output, and not exist software documentation.