Error in Running command CreateExtendedIlluminaManifest

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Nur Adlina Binti Mohd Affian

• October 03, 2022 09:21

Hi GATK team, 

I am currently generating the extended manifest file using CreateExtendedIlluminaManifest in order to use GtcToVcf (Picard) for converting gtc file to vcf. However, while running CreateExtendedIlluminaManifest. I found an error in which I could'nt find a way to solve them. Hope you may help me to resolve this error. 

REQUIRED for all errors and issues:
a) GATK version used: 

The Genome Analysis Toolkit (GATK) v4.2.6.1
HTSJDK Version: 2.24.1
Picard Version: 2.27.1

b) Exact command used:

java -jar /usr/local/bin/picard.jar CreateExtendedIlluminaManifest INPUT=ASA-24v1-0_E1.csv OUTPUT=ASA-24v1-0_E1.extended.csv REPORT_FILE=ASA-24v1-0_E1.txt CLUSTER_FILE=4th_Run.egt REFERENCE_SEQUENCE=hg19.fa 

c) Entire program log:

********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** 
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
**********    CreateExtendedIlluminaManifest -INPUT ASA-24v1-0_E1.csv -OUTPUT ASA-24v1-0_E1.extended.csv -REPORT_FILE ASA-24v1-0_E1.txt -CLUSTER_FILE 4th_Run.egt -REFERENCE_SEQUENCE hg19.fa
**********

16:51:08.285 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/synapse/Downloads/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Oct 03 16:51:08 MYT 2022] CreateExtendedIlluminaManifest INPUT=ASA-24v1-0_E1.csv OUTPUT=ASA-24v1-0_E1.extended.csv REPORT_FILE=ASA-24v1-0_E1.txt CLUSTER_FILE=4th_Run.egt REFERENCE_SEQUENCE=hg19.fa    FLAG_DUPLICATES=true TARGET_BUILD=37 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
[Mon Oct 03 16:51:08 MYT 2022] Executing as synapse@synapse-ThinkCentre-M70t on Linux 5.15.0-48-generic amd64; OpenJDK 64-Bit Server VM 11.0.16+8-post-Ubuntu-0ubuntu122.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.27.4-2-g5db8017-SNAPSHOT
INFO    2022-10-03 16:51:08    CreateExtendedIlluminaManifest    Phase 1.  First Pass through the manifest.  Build coordinate map for dupe flagging and make SNP and indel-specific interval lists for parsing dbSnp
[Mon Oct 03 16:51:08 MYT 2022] picard.arrays.illumina.CreateExtendedIlluminaManifest done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=130023424
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
    at picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator.getSequenceAt(Build37ExtendedIlluminaManifestRecordCreator.java:525)
    at picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator.calculateIsInsertionOrDeletion(Build37ExtendedIlluminaManifestRecordCreator.java:286)
    at picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator.processIndel(Build37ExtendedIlluminaManifestRecordCreator.java:239)
    at picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator.createRecord(Build37ExtendedIlluminaManifestRecordCreator.java:111)
    at picard.arrays.illumina.CreateExtendedIlluminaManifest.doWork(CreateExtendedIlluminaManifest.java:188)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:309)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

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• 

  Anthony DiCi

  • October 05, 2022 16:37

  Hi Nur Adlina Binti Mohd Affian,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.

  I brought this to our developers and received some feedback and next steps for you. It appears that you may be having a dictionary mismatch issue. In order to avoid the NullPointerException that you are encountering, the contigs must be consistent. Here are some things that you can try out.

  1. Check for a file called hg19.dict and look inside to see if there are any contigs that are not also present in your input data.

  I hope this helps! Please let me know what you find and if this leads you to success. If not, please respond to this post with both 1) the list of contigs in your fasta dictionary file (hg19.dict), and 2) the list of contigs from your main input. I can bring those back to our developers to determine the best next steps.

  Best,

  Anthony

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• 

  Anthony DiCi

  • October 13, 2022 15:25

  Hi Nur Adlina Binti Mohd Affian,

  We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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  Anthony DiCi

  • October 24, 2022 13:45

  Hi Nur Adlina Binti Mohd Affian,

  I received your reply email on the 13th. Do you have any updates? Since we haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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