The bam was created using FastqToSam, so it is unaligned. I think that's the reason why the read contig list was empty. Is there any solution for it?Thanks!
Running:
/home/kh3/Softwares/gatk/build/install/gatk/bin/gatk BwaSpark -I /home/kh3/data/Illumina/GATK4/Platinum/TEST/test.spark.sam -R /home/kh3/Resources/genome_b37/genome.fa -t 16 -O /home/kh3/data/Illumina/GATK4/Platinum/TEST/test.spark.bam
23:30:44.246 INFO IntelGKLUtils - Trying to load Intel GKL library from:
jar:file:/home/kh3/Softwares/gatk/build/install/gatk/lib/gkl-0.1.2.jar!/com/intel/gkl/native/libIntelGKL.so
23:30:44.295 INFO IntelGKLUtils - Intel GKL library loaded from classpath.
[September 15, 2016 11:30:44 PM EDT] org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark --output /home/kh3/data/Illumina/GATK4/Platinum/TEST/test.spark.bam --threads 16 --reference /home/kh3/Resources/genome_b37/genome.fa --input /home/kh3/data/Illumina/GATK4/Platinum/TEST/test.spark.sam --fixedChunkSize 100000 --readValidationStringency SILENT --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --bamPartitionSize 0 --disableSequenceDictionaryValidation false --shardedOutput false --numReducers 0 --sparkMaster local[*] --help false --version false --verbosity INFO --QUIET false --use_jdk_deflater false --disableAllReadFilters false
[September 15, 2016 11:30:44 PM EDT] Executing as kh3@rgcaahauva08091.rgc.aws.regeneron.com on Linux 3.13.0-91-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13; Version: Version:4.alpha.2-45-ga30af5a-SNAPSHOT
23:30:44.320 INFO BwaSpark - Defaults.BUFFER_SIZE : 131072
23:30:44.320 INFO BwaSpark - Defaults.COMPRESSION_LEVEL : 1
23:30:44.320 INFO BwaSpark - Defaults.CREATE_INDEX : false
23:30:44.320 INFO BwaSpark - Defaults.CREATE_MD5 : false
23:30:44.321 INFO BwaSpark - Defaults.CUSTOM_READER_FACTORY :
23:30:44.321 INFO BwaSpark - Defaults.EBI_REFERENCE_SERVICE_URL_MASK : http://www.ebi.ac.uk/ena/cram/md5/%s
23:30:44.321 INFO BwaSpark - Defaults.NON_ZERO_BUFFER_SIZE : 131072
23:30:44.321 INFO BwaSpark - Defaults.REFERENCE_FASTA : null
23:30:44.321 INFO BwaSpark - Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
23:30:44.321 INFO BwaSpark - Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:30:44.321 INFO BwaSpark - Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:30:44.321 INFO BwaSpark - Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:30:44.321 INFO BwaSpark - Defaults.USE_CRAM_REF_DOWNLOAD : false
23:30:44.321 INFO BwaSpark - Deflater IntelDeflater
23:30:44.321 INFO BwaSpark - Initializing engine
23:30:44.321 INFO BwaSpark - Done initializing engine
23:30:44.756 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
23:30:46.883 INFO BwaSpark - Shutting down engine
[September 15, 2016 11:30:46 PM EDT] org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=498597888
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605, hs37d5]
reads contigs = []
Here is the content of my input bam:
@HD VN:1.5 SO:coordinate
@RG ID:A SM:test PL:ILLUMINA
@CDDDDFHHHGHJHGHHIJJJGEGHGGFHGJIIIGIGHGGGGIGHAHGIGIBFCA(=FGGJIE;CG;AHFHFECD RG:Z:A
@FFFFFHFHFHJIIIIIJJJAEHIHIDF?BGCHEGCG*?DHGDB=DHHE@@GHGHG@EHJE>AE?B,776>A88 RG:Z:A
@FFFFFDHHGHJJJIIGGIIJGJIIGIJIBGGBDEBBFGHGGDEIDBF0CGBHIGC7=CEE=AEE@5?>(>C;; RG:Z:A