errors in installing picard

Question

[Meghan.T]

I am trying to install picard form its github repo:

git clone https://github.com/broadinstitute/picard.git
cd picard/

But when I try to build it according to the instruction ./gradlew shadowJar I get the following errors:

FAILURE: Build failed with an exception.

   What went wrong:
A problem occurred configuring root project 'picard'.
Could not resolve all files for configuration ':classpath'.
   Could not resolve org.ajoberstar.grgit:grgit-gradle:5.2.0.
     Required by:
         project : > org.ajoberstar.grgit:org.ajoberstar.grgit.gradle.plugin:5.2.0
 No matching variant of org.ajoberstar.grgit:grgit-gradle:5.2.0 was found. The consumer was configured to find a library for use during runtime, compatible with Java 8, packaged as a jar, and its dependencies declared externally, as well as attribute 'org.gradle.plugin.api-version' with value '8.5' but:
          - Variant 'apiElements' capability org.ajoberstar.grgit:grgit-gradle:5.2.0 declares a library, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares a component for use during compile-time, compatible with Java 11 and the consumer needed a component for use during runtime, compatible with Java 8
              - Other compatible attribute:
                  - Doesn't say anything about org.gradle.plugin.api-version (required '8.5')
          - Variant 'javadocElements' capability org.ajoberstar.grgit:grgit-gradle:5.2.0 declares a component for use during runtime, and its dependencies declared externally:
              - Incompatible because this component declares documentation and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about its target Java version (required compatibility with Java 8)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about org.gradle.plugin.api-version (required '8.5')
          - Variant 'runtimeElements' capability org.ajoberstar.grgit:grgit-gradle:5.2.0 declares a library for use during runtime, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares a component, compatible with Java 11 and the consumer needed a component, compatible with Java 8
              - Other compatible attribute:
                  - Doesn't say anything about org.gradle.plugin.api-version (required '8.5')
          - Variant 'sourcesElements' capability org.ajoberstar.grgit:grgit-gradle:5.2.0 declares a component for use during runtime, and its dependencies declared externally:
              - Incompatible because this component declares documentation and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about its target Java version (required compatibility with Java 8)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about org.gradle.plugin.api-version (required '8.5')
 Could not find org.ajoberstar.grgit:grgit-core:3.1.1.
     Searched in the following locations:
       - https://repo.maven.apache.org/maven2/org/ajoberstar/grgit/grgit-core/3.1.1/grgit-core-3.1.1.pom
       - https://plugins.gradle.org/m2/org/ajoberstar/grgit/grgit-core/3.1.1/grgit-core-3.1.1.pom
     Required by:
         project : > org.ajoberstar.git-publish:org.ajoberstar.git-publish.gradle.plugin:2.1.1 > org.ajoberstar:gradle-git-publish:2.1.1

Try:
Run with --stacktrace option to get the stack trace.
Run with --info or --debug option to get more log output.
Run with --scan to get full insights.
 Get more help at https://help.gradle.org.

BUILD FAILED in 24s

I have checked and I have Java 17 installed ( when I try java -version I get version 17 ), I was wondering if someone had the same issue and was able to fix it. I would also appreciate any advice you have about this.

Answer 1

[Pierre Lindenbaum]

not a solution but the jar is already available for download here: https://github.com/broadinstitute/picard/releases/download/3.3.0/picard.jar

[Meghan.T]

Thank you for your response. Th issue I have with the picard.jar file is, when I try to run markduplicates like this java -jar ~/picard.jar MarkDuplicates -I alignment.sort.bam -O dedup.bam -M metrics.txt -VALIDATION_STRINGENCY LENIENT -REMOVE_DUPLICATES true I get the following errors:

16:33:11.253 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/pt689/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Oct 21 16:33:26 EDT 2024] MarkDuplicates --INPUT alignment.sort.bam --OUTPUT dedup.bam --METRICS_FILE metrics.txt --REMOVE_DUPLICATES true --VALIDATION_STRINGENCY LENIENT --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_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_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 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 21 16:33:37 EDT 2024] Executing as pt689@argos6 on Linux 4.4.0-173-generic amd64; Java HotSpot(TM) 64-Bit Server VM 17.0.12+8-LTS-286; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO    2024-10-21 16:33:38 MarkDuplicates  Start of doWork freeMemory: 377720336; totalMemory: 402653184; maxMemory: 32178700288
INFO    2024-10-21 16:33:38 MarkDuplicates  Reading input file and constructing read end information.
INFO    2024-10-21 16:33:38 MarkDuplicates  Will retain up to 116589493 data points before spilling to disk.
[Mon Oct 21 16:33:41 EDT 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.56 minutes.
Runtime.totalMemory()=1795162112
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "htsjdk.samtools.SAMReadGroupRecord.getReadGroupId()" because the return value of "htsjdk.samtools.SAMRecord.getReadGroup()" is null
    at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:558)
    at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:270)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:115)

[GenoMax]

Did you create ReadGroups when you made the BAM? See: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups

If you did not then you will need to add them.

[Pierre Lindenbaum]

this is unrelated to your original question, please close that one and ask a new question.

[Meghan.T]

Did you mean to delete the post? I can't find a close option unfortunately.

[GenoMax]

Not delete this post. Pierre was asking you to post the comment above with the error as a new question since it is not related to your original post.

[Meghan.T]

Oh,I see. I'll do that.