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File not found while executing CollectHsMetric on GATK 4.1.2.0

I am executing this command

time gatk CollectHsMetrics -I test.bam -O hs_metrics.txt  -R genome.fa -BAIT_INTERVALS Target_bait.bed.interval.list -TARGET_INTERVALS Exome_Target_hg19.interval_list 

I am getting this error

Using GATK jar /home/bioinfo/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/bioinfo/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar CollectHsMetrics -I test.bam -O hs_metrics.txt -R genome.fa -BAIT_INTERVALS Target_bait.bed.interval.list -TARGET_INTERVALS Exome_Target_hg19.interval_list
19:05:20.489 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/bioinfo/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Oct 07 19:05:20 IST 2019] CollectHsMetrics  --BAIT_INTERVALS Target_bait.bed.interval.list --TARGET_INTERVALS Exome_Target_hg19.interval_list --INPUT test.bam --OUTPUT hs_metrics.txt --REFERENCE_SEQUENCE genome.fa  --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Oct 07, 2019 7:05:22 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Mon Oct 07 19:05:22 IST 2019] Executing as [email protected] on Linux 4.15.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_222-8u222-b10-1ubuntu1~16.04.1-b10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.2.0
[Mon Oct 07 19:05:22 IST 2019] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=726138880
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMException: Cannot read non-existent file: file:///media/bioinfo/@HD%09VN:1.6%09SO:coordinate
    at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405)
    at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392)
    at picard.analysis.directed.CollectHsMetrics.getProbeIntervals(CollectHsMetrics.java:146)
    at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:129)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)

real    0m3.631s
user    0m8.760s
sys 0m0.307s

Answers

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