Process `NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES

[wangjiaming1503]

Description of the bug

12月-01 08:35:42.217 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1); work-dir=/home/data/linli/七月份果糖/gz/original/test/work/fe/10916a2fc6f1b328c2d3d20f57b396
error [nextflow.exception.ProcessFailedException]: Process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1) terminated with an error exit status (1)
12月-01 08:35:42.240 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)'

Caused by:
Process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1) terminated with an error exit status (1)

Command executed:

picard
-Xmx4915M
MarkDuplicates
--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp
--INPUT RAP1_UNINDUCED_REP1.sorted.bam
--OUTPUT RAP1_UNINDUCED_REP1.markdup.sorted.bam
--REFERENCE_SEQUENCE genome_gfp.fasta
--METRICS_FILE RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES":
picard: $(echo $(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS

Command exit status:
1

Command output:
2023-12-01 00:35:41,533 main WARN JMX runtime input lookup class is not available because this JRE does not support JMX. JMX lookups will not be available, continuing configuration. Ignoring java.lang.IllegalArgumentException: java.lang.NoClassDefFoundError: Could not initialize class org.apache.logging.log4j.core.lookup.JmxRuntimeInputArgumentsLookup
2023-12-01 00:35:41,586 main ERROR Could not reconfigure JMX java.lang.NoClassDefFoundError: Could not initialize class java.lang.management.ManagementFactory$PlatformMBeanFinder
at java.management/java.lang.management.ManagementFactory.platformComponents(ManagementFactory.java:915)
at java.management/java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:485)
at org.apache.logging.log4j.core.jmx.Server.reregisterMBeansAfterReconfigure(Server.java:140)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:637)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:699)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:155)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:196)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:599)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:585)
at org.broadinstitute.barclay.argparser.ClassFinder.(ClassFinder.java:29)
at picard.cmdline.PicardCommandLine.processAllCommandLinePrograms(PicardCommandLine.java:178)
at picard.cmdline.PicardCommandLine.extractCommandLineProgram(PicardCommandLine.java:121)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:99)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)

Command error:
00:35:41.872 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.0.0-1/picard.jar!/com/intel/gkl/native/libgkl_compression.so
00:35:41.872 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
[Fri Dec 01 00:35:41 GMT 2023] MarkDuplicates --INPUT RAP1_UNINDUCED_REP1.sorted.bam --OUTPUT RAP1_UNINDUCED_REP1.markdup.sorted.bam --METRICS_FILE RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE genome_gfp.fasta --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 --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --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 --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Dec 01 00:35:41 GMT 2023] Executing as linl@54bbcb906c28 on Linux 5.15.0-89-generic amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Jdk; Inflater: Jdk; Provider GCS is not available; Picard version: Version:3.0.0
[Fri Dec 01 00:35:41 GMT 2023] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=109051904
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/data/linli/%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F/gz/original/test/work/fe/10916a2fc6f1b328c2d3d20f57b396/RAP1_UNINDUCED_REP1.sorted.bam
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:498)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:485)
at htsjdk.samtools.util.IOUtil.assertInputIsValid(IOUtil.java:461)
at htsjdk.samtools.util.IOUtil.assertInputsAreValid(IOUtil.java:537)
at Ignoring java.lang.IllegalArgumentException: java.lang.NoClassDefFoundError: Could not initialize class org.apache.logging.log4j.core.lookup.JmxRuntimeInputArgumentsLookup
2023-12-01 00:35:41,586 main ERROR Could not reconfigure JMX java.lang.NoClassDefFoundError: Could not initialize class java.lang.management.ManagementFactory$PlatformMBeanFinder
at java.management/java.lang.management.ManagementFactory.platformComponents(ManagementFactory.java:915)
at java.management/java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:485)
at org.apache.logging.log4j.core.jmx.Server.reregisterMBeansAfterReconfigure(Server.java:140)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:637)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:699)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:155)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:196)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:599)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:585)
at org.broadinstitute.barclay.argparser.ClassFinder.(ClassFinder.java:29)
at picard.cmdline.PicardCommandLine.processAllCommandLinePrograms(PicardCommandLine.java:178)
at picard.cmdline.PicardCommandLine.extractCommandLineProgram(PicardCommandLine.java:121)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:99)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)

00:35:41.850 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.0.0-1/picard.jar!/com/intel/gkl/native/libgkl_compression.so
00:35:41.871 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
00:35:41.872 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.0.0-1/picard.jar!/com/intel/gkl/native/libgkl_compression.so
00:35:41.872 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
[Fri Dec 01 00:35:41 GMT 2023] MarkDuplicates --INPUT RAP1_UNINDUCED_REP1.sorted.bam --OUTPUT RAP1_UNINDUCED_REP1.markdup.sorted.bam --METRICS_FILE RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE genome_gfp.fasta --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 --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --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 --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Dec 01 00:35:41 GMT 2023] Executing as linl@54bbcb906c28 on Linux 5.15.0-89-generic amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Jdk; Inflater: Jdk; Provider GCS is not available; Picard version: Version:3.0.0
[Fri Dec 01 00:35:41 GMT 2023] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=109051904
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/data/linli/%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F/gz/original/test/work/fe/10916a2fc6f1b328c2d3d20f57b396/RAP1_UNINDUCED_REP1.sorted.bam
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:498)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:485)
at htsjdk.samtools.util.IOUtil.assertInputIsValid(IOUtil.java:461)
at htsjdk.samtools.util.IOUtil.assertInputsAreValid(IOUtil.java:537)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:257)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:104)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)

Work dir:
/home/data/linli/七月份果糖/gz/original/test/work/fe/10916a2fc6f1b328c2d3d20f57b396

Command used and terminal output

2023-12-01 08:32:52	4m 18s	elated_monod	ERR	a10f41afa204538d5dcc89a5910c299d68f94f41	6c7efdbf-e7c5-406d-93c6-96f30369cfa9	nextflow run nf-core/rnaseq -profile test,docker --outdir /home/linl/data_linli/七月份果糖/gz/original/test -r 3.13.2

Relevant files

.nextflow.log

System information

Version: 23.10.0 build 5889
Created: 15-10-2023 15:07 UTC (23:07 CDT)
System: Linux 5.15.0-89-generic
Executor： local
Container engine Docker
Version of nf-core/rnaseq 3.13.2

[wangjiaming1503]

The issue has been resolved! It was discovered that some programs in the pipeline do not support Chinese characters in file paths. Therefore, it is recommended to avoid using Chinese words in the paths. The original working directory was:

/home/data/linli/七月份果糖/gz/original/test/work/fe/10916a2fc6f1b328c2d3d20f57b396

To fix the problem, it is suggested to change the path to:

/home/linl/data_linli/Fru_July/gz/original

By removing the Chinese characters from the path, the issue should be resolved. If anyone encounters a similar problem, please check the file path for the presence of Chinese characters.

The exception message indicates that the program cannot read a non-existent file, and the Chinese characters in the original path were replaced with "%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F%3F". It seems that the program does not handle Chinese characters properly.

In summary, the recommended solution is to modify the issue by excluding Chinese characters from the file paths to ensure proper support by the programs.