Picard's Tool MarkDuplicates problem

Question

[harmadikemil]

Dear all!

I try to use Picard's tool, but I always get an error code.

I used the first version, and get a note (the tool didn't work after it). The second type of syntax i get an error code. What should be the solution for it?

java -jar /data/tools/java/picard.jar MarkDuplicates I=PLEper56_MT_S7_R1_001.fastq.gz.sorted.bam O=PLEper56_MT_S7_R1_001.fastq.gz.cleaned.bam M=PLEper56_MT_S7_R1_001.fastq.gz.marked_dup_metrics.txt REMOVE_DUPLICATES=TRUE ASSUME_SORTED=TRUE
NOTE: Picard's command line syntax is changing.
java -jar /data/tools/java/picard.jar MarkDuplicates -I PLEper56_MT_S7_R1_001.fastq.gz.sorted.bam -O PLEper56_MT_S7_R1_001.fastq.gz.cleaned.bam -M PLEper56_MT_S7_R1_001.fastq.gz.marked_dup_metrics.txt -REMOVE_DUPLICATES TRUE -ASSUME_SORTED TRUE
ERROR: Invalid argument '-I'.

[h.mon]

Please say what is the version of Picard you are using.

I used the first version, and get a note (the tool didn't work after it).

The syntax deprecation note is not the cause of Picard not working. If it didn't work, along the note there should be an error message explaining the cause of the error.

[harmadikemil]

2.21.3-SNAPSHOT is the Picard's version

this is the whole log:

** NOTE: Picard's command line syntax is changing.

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** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

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** The command line looks like this in the new syntax:

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** MarkDuplicates -I PLEper56_MT_S7_R1_001.fastq.gz.sorted.bam -O PLEper56_MT_S7_R1_001.fastq.gz.cleaned.bam -M PLEper56_MT_S7_R1_001.fastq.gz.marked_dup_metrics.txt -REMOVE_DUPLICATES TRUE -ASSUME_SORTED TRUE

---

09:15:41.789 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/tools/java/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Feb 19 09:15:41 CET 2020] MarkDuplicates INPUT=[PLEper56_MT_S7_R1_001.fastq.gz.sorted.bam] OUTPUT=PLEper56_MT_S7_R1_001.fastq.gz.cleaned.bam METRICS_FILE=PLEper56_MT_S7_R1_001.fastq.gz.marked_dup_metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture="" of="" last="" three="" ':'="" separated="" fields="" as="" numeric="" values=""> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Feb 19 09:15:41 CET 2020] Executing as enyerki@archeo on Linux 4.18.0-80.el8.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_232-b09; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.21.3-SNAPSHOT [Wed Feb 19 09:15:41 CET 2020] picard.sam.markduplicates.MarkDuplicates 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:///data/analysis/MT-NEW/run22-single/test/PLEper56_MT_S7_R1_001.fastq.gz.sorted.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:483) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:470) at htsjdk.samtools.util.IOUtil.assertInputIsValid(IOUtil.java:446) at htsjdk.samtools.util.IOUtil.assertInputsAreValid(IOUtil.java:522) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:249) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) 256

[h.mon]

Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///data/analysis/MT-NEW/run22-single/test/PLEper56_MT_S7_R1_001.fastq.gz.sorted.

The file name or path to the file is incorrect.