picard报错的问题

picard报错的问题

parallel --will-cite --jobs 2 --delay 0.5 'picard MarkDuplicates
INPUT={}
OUTPUT={.}.rmdup
METRICS_FILE={.}.dups.log
REMOVE_DUPLICATES=true
BARCODE_TAG=RG
TMP_DIR=/mnt/f/temp/ ’ ::: SubBarcodes.$Name.$Species.*.bam

#####失败报错 Name的问题
Name=SubBarcodes.sp.atac.first
Species=hg19
parallel --will-cite --jobs 2 --delay 0.5 'picard MarkDuplicates INPUT={} OUTPUT={.}.rmdup METRICS_FILE={.}.dups.log ’ ::: SubBarcodes.$Name.$Species.*.bam

###成功的话
picard MarkDuplicates INPUT=“SubBarcodes.sp.atac.first.hg19.0000.bam” OUTPUT=“test.bam” METRICS_FILE=“test.dups.log”
picard MarkDuplicates INPUT=“SubBarcodes.sp.atac.first.hg19.0000.bam” OUTPUT=“test2.bam” METRICS_FILE=“test2.dups.log” REMOVE_DUPLICATES=“true”

#####这个又成功
Name=SubBarcodes.sp.atac.first
Species=hg19
parallel --will-cite --jobs 2 --delay 0.5 'picard MarkDuplicates INPUT={} OUTPUT={.}.rmdup METRICS_FILE={.}.dups.log ’ ::: SubBarcodes.sp.atac.first.hg19.0000.bam

#####失败 BARCODE_TAG=RG 问题
Name=sp.atac.first
Species=hg19
parallel --will-cite --jobs 2 --delay 0.5 'picard MarkDuplicates INPUT={} OUTPUT={.}.rmdup METRICS_FILE={.}.dups.log REMOVE_DUPLICATES=true BARCODE_TAG=RG ’ ::: SubBarcodes.sp.atac.first.hg19.0000.bam

picard MarkDuplicates INPUT=“SubBarcodes.sp.atac.first.hg19.0000.bam” OUTPUT=“test2.bam” METRICS_FILE=“test2.dups.log” REMOVE_DUPLICATES=“true” BARCODE_TAG=“RG”
picard MarkDuplicates INPUT=“SubBarcodes.sp.atac.first.hg19.0000.bam” OUTPUT=“test2.bam” METRICS_FILE=“test2.dups.log” REMOVE_DUPLICATES=“true” BARCODE_TAG=RG

(rna) yyp@DESKTOP-LRUCLJJ:~/picard-master$ parallel --will-cite --jobs 2 --delay 0.5 'picard MarkDuplicates INPUT={} OUTPUT={.}.rmdup METRICS_FILE={.}.dups.log REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT BARCODE_TAG=RG TMP_DIR='$di{r}^{\prime }/temp{/}^{\prime }:::SubBarcodes.$Name.$Species.*.bam
INFO 2021-10-31 19:35:12 MarkDuplicates

********** 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:

---

********** MarkDuplicates -INPUT SubBarcodes….bam -OUTPUT SubBarcodes….rmdup -METRICS_FILE SubBarcodes…*.dups.log -REMOVE_DUPLICATES true -VALIDATION_STRINGENCY SILENT -BARCODE_TAG RG -TMP_DIR /temp/

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19:35:12.981 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/yyp/miniconda3/envs/rna/share/picard-2.18.29-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
19:35:12.988 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
19:35:12.989 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/yyp/miniconda3/envs/rna/share/picard-2.18.29-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
19:35:12.990 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
[Sun Oct 31 19:35:12 CST 2021] MarkDuplicates BARCODE_TAG=RG INPUT=[SubBarcodes….bam] OUTPUT=SubBarcodes….rmdup METRICS_FILE=SubBarcodes….dups.log REMOVE_DUPLICATES=true TMP_DIR=[/temp] VALIDATION_STRINGENCY=SILENT 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 ASSUME_SORTED=false 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 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
[Sun Oct 31 19:35:12 CST 2021] Executing as yyp@DESKTOP-LRUCLJJ on Linux 4.19.128-microsoft-standard amd64; OpenJDK 64-Bit Server VM 10.0.2+13; Deflater: Jdk; Inflater: Jdk; Provider GCS is not available; Picard version: 2.18.29-SNAPSHOT
[Sun Oct 31 19:35:12 CST 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=536870912
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:///home/yyp/picard-master/SubBarcodes….bam
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:432)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:419)
at htsjdk.samtools.util.IOUtil.assertInputIsValid(IOUtil.java:395)
at htsjdk.samtools.util.IOUtil.assertInputsAreValid(IOUtil.java:471)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:256)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
(rna) yyp@DESKTOP-LRUCLJJ:~/picard-master$