Everything looks "fine" when running RNA-SeQC, but RPKMs of all genes are zero! Could anyone help me

Could anyone help me? I used STAR to do mapping and got the orded BAM file, and have added RG tag, Markdupicate and Index by picard successfully. But encounter problem when running RNA-SeQC(1.19).Everything in log file looks "fine" , but RPKMs of all genes are zero! I check the gtf and reference carefully, but they look good. Could anyone see any error in my log information? Thanks in advance!

---- COMMAND EXECUTED: ---------------------------------------------------------

java -jar Softs/RNA-SeQC.jar -n 1000 -s 153_R1,153_R1Aligned.sortedByCoord.out.RG.dedup.bam,153_R1 -t gencode.v19.genes.v7.patched_contigs.gtf -r Homo_sapiens_assembly19.fasta -o ./RNA-SeQC_out22 -noDoC -strictMode

RNA-SeQC v1.1.9 06/26/16
Creating rRNA Interval List based on given GTF annotations
Retriving contig names from reference
contig names in reference: 85
Loading GTF for Read Counting
Converting to refGene
Transcript objects to RefGen format: 1 s
Running IntronicExpressionReadBlock Walker ....
Arguments: [-T, IntronicExpressionReadBlockWalker, --outfile_metrics, ./RNA-SeQC_out22/153_R1/153_R1, -R, Homo_sapiens_assembly19.fasta, -I, 153_R1Aligned.sortedByCoord.out.RG.dedup.bam, -strict, -refseq, ./RNA-SeQC_out22/refGene.txt, -l, ERROR]
Finished writing ./RNA-SeQC_out22/153_R1/153_R1.exon_intron_report.txt
Finished writing ./RNA-SeQC_out22/153_R1/153_R1.intron_report.txt, now creating RPKM values for introns ..
GATK command result code: 0
... GATK CoutReadMetrics Analysis DONE
CountReadMetricsWalker Runtime: 25 min
Counting rRNA reads
Running OutputCountReads Walker ....
Arguments: [-T, OutputCountReadsWalker, --outfile_readCounts, ./RNA-SeQC_out22/153_R1/153_R1.rRNA_counts.txt, -R, Homo_sapiens_assembly19.fasta, -I, 153_R1Aligned.sortedByCoord.out.RG.dedup.bam, -L, ./RNA-SeQC_out22/rRNA_intervals.list, -l, ERROR]
GATK command result code: 0
... GATK CoutReadMetrics Analysis DONE (file:./RNA-SeQC_out22/153_R1/153_R1.rRNA_counts.txt)
CountReadMetricsWalker (rRNA) Runtime for MAYO_153_R1: 0 min
Calculating library complexity for MAYO_153_R1
Libary Complexity Calculation Time: 710 s
Finished Successfully.

RNA-SeQC Total Runtime: 37 min

The following are metric file, all the RPKM are zero.


56202 1
Name Description 153_R1
ENSG00000223972.4 DDX11L1 0.0
ENSG00000227232.4 WASH7P 0.0
ENSG00000243485.2 MIR1302-11 0.0
ENSG00000237613.2 FAM138A 0.0
ENSG00000268020.2 OR4G4P 0.0
ENSG00000240361.1 OR4G11P 0.0
ENSG00000186092.4 OR4F5 0.0
ENSG00000238009.2 RP11-34P13.7 0.0
ENSG00000233750.3 CICP27 0.0
ENSG00000237683.5 AL627309.1 0.0
ENSG00000268903.1 RP11-34P13.15 0.0
ENSG00000239906.1 RP11-34P13.14 0.0
ENSG00000241860.2 RP11-34P13.13 0.0
ENSG00000222623.1 RNU6-1100P 0.0
ENSG00000241599.1 RP11-34P13.9 0.0
ENSG00000228463.4 AP006222.2 0.0
ENSG00000237094.7 RP4-669L17.10 0.0
ENSG00000250575.1 RP4-669L17.8 0.0
ENSG00000233653.3 CICP7 0.0
ENSG00000224813.2 RP4-669L17.4 0.0
ENSG00000235249.1 OR4F29 0.0
ENSG00000269732.1 WBP1LP7 0.0
ENSG00000256186.1 AL732372.1 0.0
ENSG00000236601.1 RP4-669L17.2 0.0
ENSG00000236743.1 RP5-857K21.15 0.0
ENSG00000236679.2 RP4-669L17.1 0.0
ENSG00000231709.1 RP5-857K21.1 0.0
ENSG00000235146.2 RP5-857K21.2 0.0
ENSG00000239664.2 RP5-857K21.3 0.0
ENSG00000230021.3 RP5-857K21.4 0.0


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