Hi,

I am trying to generate coverage per gene statistics but keep getting an error. I have prepare the refseq file according to Refseq gene list. I have got 8 output files. _gene_summary file was generated but contains header with gene names/no statistics and _gene_statistics file was not generated. The other looks fine. Could you help me figure out what is the problem please?

Thank you!!

GATK v4.1.9.0

command used:

gatk DepthOfCoverage \
-R Mus_musculus.GRCm38.dna_sm.primary_assembly.fa \
-O 153DoC \
-I 153.bam \
-gene-list genetrack.refseq \
-L Covered.bed

Error:

17:15:31.661 INFO  DepthOfCoverage - ------------------------------------------------------------

17:15:31.662 INFO  DepthOfCoverage - The Genome Analysis Toolkit (GATK) v4.1.9.0

17:15:31.662 INFO  DepthOfCoverage - For support and documentation go to https://software.broadinstitute.org/gatk/

17:15:31.664 INFO  DepthOfCoverage - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-b11

17:15:31.664 INFO  DepthOfCoverage - Start Date/Time: February 4, 2021 5:15:29 PM AEST

17:15:31.664 INFO  DepthOfCoverage - ------------------------------------------------------------

17:15:31.664 INFO  DepthOfCoverage - ------------------------------------------------------------

17:15:31.665 INFO  DepthOfCoverage - HTSJDK Version: 2.23.0

17:15:31.665 INFO  DepthOfCoverage - Picard Version: 2.23.3

17:15:31.665 INFO  DepthOfCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 2

17:15:31.665 INFO  DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

17:15:31.665 INFO  DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

17:15:31.665 INFO  DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

17:15:31.666 INFO  DepthOfCoverage - Deflater: IntelDeflater

17:15:31.666 INFO  DepthOfCoverage - Inflater: IntelInflater

17:15:31.666 INFO  DepthOfCoverage - GCS max retries/reopens: 20

17:15:31.666 INFO  DepthOfCoverage - Requester pays: disabled

17:15:31.666 WARN  DepthOfCoverage - 

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: DepthOfCoverage is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

17:15:31.666 INFO  DepthOfCoverage - Initializing engine

17:15:32.418 INFO  FeatureManager - Using codec BEDCodec to read file file:///Covered.bed

17:15:32.487 INFO  IntervalArgumentCollection - Processing 485336 bp from intervals

17:15:32.497 INFO  DepthOfCoverage - Done initializing engine

17:15:32.572 INFO  ProgressMeter - Starting traversal

17:15:32.572 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute

17:15:33.074 INFO  FeatureManager - Using codec BEDCodec to read file file:///Covered.bed

17:15:33.128 INFO  FeatureManager - Using codec RefSeqCodec to read file file:///genetrack.refseq

17:15:33.131 WARN  Utils - **********************************************************************

17:15:33.132 WARN  Utils - * WARNING:

17:15:33.132 WARN  Utils - * 

17:15:33.132 WARN  Utils - * RefSeq file contains transcripts with zero coding length. Such

17:15:33.132 WARN  Utils - * transcripts will be ignored (this warning is printed only once)

17:15:33.132 WARN  Utils - **********************************************************************

17:15:42.654 INFO  ProgressMeter -           1:86070579              0.2                  6000          35707.2

17:15:58.103 INFO  ProgressMeter -           1:88218427              0.4                 11000          25850.9

17:16:09.290 INFO  ProgressMeter -          1:169987087              0.6                 19000          31047.4

17:16:19.834 INFO  ProgressMeter -          10:26986836              0.8                 26000          33007.5

17:16:30.637 INFO  ProgressMeter -          10:27350407              1.0                 35000          36167.0

17:16:41.546 INFO  ProgressMeter -          10:52194843              1.1     

# here is the first few lines of the refseq file
#bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
1082	NM_001111320	chr1	-	65158615	65186479	65159464	65175352	9	65158615,65161049,65161799,65165099,65166106,65168498,65170958,65175230,65186304,	65159555,65161212,65161940,65165251,65166284,65168604,65171250,65175368,65186479,	0	Idh1	cmpl	cmpl	2,1,1,2,1,0,2,0,-1,
222	NM_001136104	chr1	+	156558786	156649619	156559048	156642716	13	156558786,156620838,156622484,156625287,156629852,156631344,156633079,156633752,156635064,156636817,156640438,156640992,156641541,	156559205,156620901,156622655,156625583,156630125,156631429,156633257,156633937,156635217,156636907,156640612,156641229,156649619,	0	Abl2	cmpl	cmpl	0,1,1,1,0,0,1,2,1,1,1,1,1,
1863	NM_001159731	chr1	+	167618264	167639623	167624999	167639273	9	167618264,167624927,167627291,167630961,167631229,167632514,167634434,167635699,167639125,	167618495,167625072,167627471,167631122,167631359,167632647,167634526,167635805,167639623,	0	Rxrg	cmpl	cmpl	-1,0,1,1,0,1,2,1,2,
1591	NM_001177628	chr1	+	131962914	131982972	131976940	131981728	5	131962914,131976717,131977412,131978747,131981290,