Help with picard
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Entering edit mode
6 weeks ago
Cony Lab • 0

Can anyone help me? I have no idea why my Picard not working. I used to make it work but now when I run a pipeline, this picard step can't work.

Thank you so much!

 (R-4) $ java -jar picard.jar CollectRawWgsMetrics -R /ref/hs37d5.fa -I CPM00002066-PL-D-20191015_20211104-dragen-somatic_tumor.bam -O coverage/name.txt
23:06:53.901 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/fs1/home/jietingh/picard/pi
card.jar!/com/intel/gkl/native/libgkl_compression.so
[Sat Dec 04 23:06:53 PST 2021] CollectRawWgsMetrics --INPUT /gpfs/fs1/jietingh/CPM00002066-PL-D-20191015_20211104-drag
en-somatic_tumor.bam --OUTPUT coverage/name.txt --REFERENCE_SEQUENCE /gpfs/fs1/home/cpmuser/ref/hs37d5.fa --MINIMUM_MA
PPING_QUALITY 0 --MINIMUM_BASE_QUALITY 3 --COVERAGE_CAP 100000 --LOCUS_ACCUMULATION_CAP 200000 --STOP_AFTER -1 --INCLU
DE_BQ_HISTOGRAM false --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALL
ELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_F
RACTION 0.3 --ALLELE_FRACTION 0.5 --USE_FAST_ALGORITHM false --READ_LENGTH 150 --VERBOSITY INFO --QUIET false --VALIDA
TION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Sat Dec 04 23:06:53 PST 2021] Executing as @chla-cpm-login on Linux 3.10.0-327.el7.x86_64 amd64; OpenJDK 64-B
it Server VM 1.8.0_92-b15; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.
26.6
[Sat Dec 04 23:06:53 PST 2021] picard.analysis.CollectRawWgsMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///gpfs/fs1/jietingh/CPM0
0002066-PL-D-20191015_20211104-dragen-somatic_tumor.bam
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:498)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:485)
at picard.analysis.CollectWgsMetrics.doWork(CollectWgsMetrics.java:189)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
picard Help with • 301 views
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Entering edit mode
6 weeks ago
patrickdm ▴ 40

Cannot read non-existent file: file:///gpfs/fs1/jietingh/CPM0 0002066-PL-D-20191015_20211104-dragen-somatic_tumor.bam

I'm just guessing here but It looks like there is an invisible space character (zero width space?) between CPM0 and the following part of the input file name 0002066-PL-[..] in your command's param -I CPM00002066-PL-D-20191015_20211104-dragen-somatic_tumor.bam. Hth

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