{"action":"created","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2453","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2453/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2453/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2453/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2453","id":341548788,"node_id":"MDU6SXNzdWUzNDE1NDg3ODg=","number":2453,"title":"fatal error has been detected by the Java Runtime Environment","user":{"login":"komalsrathi","id":7000615,"node_id":"MDQ6VXNlcjcwMDA2MTU=","avatar_url":"https://avatars3.githubusercontent.com/u/7000615?v=4","gravatar_id":"","url":"https://api.github.com/users/komalsrathi","html_url":"https://github.com/komalsrathi","followers_url":"https://api.github.com/users/komalsrathi/followers","following_url":"https://api.github.com/users/komalsrathi/following{/other_user}","gists_url":"https://api.github.com/users/komalsrathi/gists{/gist_id}","starred_url":"https://api.github.com/users/komalsrathi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/komalsrathi/subscriptions","organizations_url":"https://api.github.com/users/komalsrathi/orgs","repos_url":"https://api.github.com/users/komalsrathi/repos","events_url":"https://api.github.com/users/komalsrathi/events{/privacy}","received_events_url":"https://api.github.com/users/komalsrathi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-16T14:44:01Z","updated_at":"2018-07-19T15:01:29Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI am facing another issue related to Java. I have tried this on 3 different servers, with different memory and core settings but all have the same problem. Here are the logs: \r\n[logs.txt](https://github.com/bcbio/bcbio-nextgen/files/2198051/logs.txt)\r\n\r\nHere is my command:\r\n```\r\n/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/local/bin/bcbio_nextgen.py config.yaml -n 20\r\n```\r\n\r\nConfig file:\r\n\r\n```\r\ndetails:\r\n- algorithm:\r\n    aligner: star\r\n    variantcaller: gatk-haplotype\r\n    # tools_off: gatk4\r\n  analysis: RNA-seq\r\n  description: 'Sample 1: CDL-634-13P'\r\n  files:\r\n  - /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/fastq/CDL-634-13P/CDL-634-13P_pe_1.fq.gz\r\n  - /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/fastq/CDL-634-13P/CDL-634-13P_pe_2.fq.gz\r\n  genome_build: GRCh37\r\n  metadata:\r\n    batch: CDL-634-13P\r\nfc_name: CDL-634-13P-CDLS\r\nupload:\r\n  dir: /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/final\r\nresources:\r\n  gatk:\r\n    jvm_opts: [\"-Xms2g\", \"-Xmx4g\"]\r\n```\r\n\r\nAlso, if there is no way this can be fixed then as an alternative how can I skip this step? My goal is to finish the pipeline and just get variant calls in a normal vcf format (I also don't care about the gvcf) from a single sample.\r\n"},"comment":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/comments/406307762","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2453#issuecomment-406307762","issue_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2453","id":406307762,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNjMwNzc2Mg==","user":{"login":"komalsrathi","id":7000615,"node_id":"MDQ6VXNlcjcwMDA2MTU=","avatar_url":"https://avatars3.githubusercontent.com/u/7000615?v=4","gravatar_id":"","url":"https://api.github.com/users/komalsrathi","html_url":"https://github.com/komalsrathi","followers_url":"https://api.github.com/users/komalsrathi/followers","following_url":"https://api.github.com/users/komalsrathi/following{/other_user}","gists_url":"https://api.github.com/users/komalsrathi/gists{/gist_id}","starred_url":"https://api.github.com/users/komalsrathi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/komalsrathi/subscriptions","organizations_url":"https://api.github.com/users/komalsrathi/orgs","repos_url":"https://api.github.com/users/komalsrathi/repos","events_url":"https://api.github.com/users/komalsrathi/events{/privacy}","received_events_url":"https://api.github.com/users/komalsrathi/received_events","type":"User","site_admin":false},"created_at":"2018-07-19T15:01:29Z","updated_at":"2018-07-19T15:01:29Z","author_association":"NONE","body":"Hi,\r\n\r\nHere is the log when I run it in stand alone mode:\r\n\r\n```\r\n# grep the failing command\r\n[rathik@reslnrefo01 log]$ grep GenomicsDB bcbio-nextgen-commands.log\r\n[2018-07-19T06:30Z] unset JAVA_HOME && export PATH=/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms454m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/joint/gatk-haplotype-joint/CDL-164-04P/1/bcbiotx/tmpnSYdjf' GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path CDL-164-04P-1_0_249250621_genomicsdb -L 1:1-249250621 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/variation/rnaseq/gatk-haplotype/Sample_1__CDL-164-04P-gatk-haplotype-annotated-rnaedit-annotated-gemini.vcf.gz\r\n\r\n# run the command\r\n[rathik@reslnrefo01 log]$ unset JAVA_HOME && export PATH=/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms454m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/joint/gatk-haplotype-joint/CDL-164-04P/1/bcbiotx/tmpnSYdjf' GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path CDL-164-04P-1_0_249250621_genomicsdb -L 1:1-249250621 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/variation/rnaseq/gatk-haplotype/Sample_1__CDL-164-04P-gatk-haplotype-annotated-rnaedit-annotated-gemini.vcf.gz\r\nUsing GATK jar /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/share/gatk4-4.0.6.0-0/gatk-package-4.0.6.0-local.jar\r\nRunning:\r\n    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms454m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/joint/gatk-haplotype-joint/CDL-164-04P/1/bcbiotx/tmpnSYdjf -jar /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/share/gatk4-4.0.6.0-0/gatk-package-4.0.6.0-local.jar GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path CDL-164-04P-1_0_249250621_genomicsdb -L 1:1-249250621 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/variation/rnaseq/gatk-haplotype/Sample_1__CDL-164-04P-gatk-haplotype-annotated-rnaedit-annotated-gemini.vcf.gz\r\nPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/tmp/rathik\r\n10:58:41.778 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/share/gatk4-4.0.6.0-0/gatk-package-4.0.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so\r\n10:58:42.933 INFO  GenomicsDBImport - ------------------------------------------------------------\r\n10:58:42.934 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.6.0\r\n10:58:42.934 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/\r\n10:58:42.936 INFO  GenomicsDBImport - Executing as rathik@reslnrefo01.research.chop.edu on Linux v3.10.0-862.el7.x86_64 amd64\r\n10:58:42.937 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_144-b01\r\n10:58:42.937 INFO  GenomicsDBImport - Start Date/Time: July 19, 2018 10:58:41 AM EDT\r\n10:58:42.937 INFO  GenomicsDBImport - ------------------------------------------------------------\r\n10:58:42.937 INFO  GenomicsDBImport - ------------------------------------------------------------\r\n10:58:42.938 INFO  GenomicsDBImport - HTSJDK Version: 2.16.0\r\n10:58:42.938 INFO  GenomicsDBImport - Picard Version: 2.18.7\r\n10:58:42.938 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2\r\n10:58:42.938 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false\r\n10:58:42.939 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true\r\n10:58:42.939 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false\r\n10:58:42.939 INFO  GenomicsDBImport - Deflater: IntelDeflater\r\n10:58:42.939 INFO  GenomicsDBImport - Inflater: IntelInflater\r\n10:58:42.939 INFO  GenomicsDBImport - GCS max retries/reopens: 20\r\n10:58:42.939 INFO  GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes\r\n10:58:42.939 INFO  GenomicsDBImport - Initializing engine\r\n10:58:44.090 INFO  IntervalArgumentCollection - Processing 249250621 bp from intervals\r\n10:58:44.123 INFO  GenomicsDBImport - Done initializing engine\r\nCreated workspace /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/log/CDL-164-04P-1_0_249250621_genomicsdb\r\n10:58:44.723 INFO  GenomicsDBImport - Vid Map JSON file will be written to CDL-164-04P-1_0_249250621_genomicsdb/vidmap.json\r\n10:58:44.723 INFO  GenomicsDBImport - Callset Map JSON file will be written to CDL-164-04P-1_0_249250621_genomicsdb/callset.json\r\n10:58:44.723 INFO  GenomicsDBImport - Complete VCF Header will be written to CDL-164-04P-1_0_249250621_genomicsdb/vcfheader.vcf\r\n10:58:44.723 INFO  GenomicsDBImport - Importing to array - CDL-164-04P-1_0_249250621_genomicsdb/genomicsdb_array\r\n10:58:44.724 INFO  ProgressMeter - Starting traversal\r\n10:58:44.724 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute\r\n10:58:45.326 INFO  GenomicsDBImport - Importing batch 1 with 1 samples\r\nBuffer resized from 22726bytes to 32529\r\nBuffer resized from 32529bytes to 32693\r\nBuffer resized from 32693bytes to 32738\r\nBuffer resized from 32738bytes to 32741\r\nBuffer resized from 32741bytes to 32756\r\nBuffer resized from 32756bytes to 32768\r\nBuffer resized from 32768bytes to 32769\r\n#\r\n# A fatal error has been detected by the Java Runtime Environment:\r\n#\r\n#  SIGSEGV (0xb) at pc=0x00007f1ab23b8fe4, pid=92028, tid=0x00007f1a9817e700\r\n#\r\n# JRE version: OpenJDK Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)\r\n# Java VM: OpenJDK 64-Bit Server VM (25.144-b01 mixed mode linux-amd64 compressed oops)\r\n# Problematic frame:\r\n# C  [libc.so.6+0x153fe4]  __memmove_ssse3+0x2834\r\n#\r\n# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try \"ulimit -c unlimited\" before starting Java again\r\n#\r\n# An error report file with more information is saved as:\r\n# /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/CDL-164-04P/log/hs_err_pid92028.log\r\n#\r\n# If you would like to submit a bug report, please visit:\r\n#   http://www.azulsystems.com/support/\r\n# The crash happened outside the Java Virtual Machine in native code.\r\n# See problematic frame for where to report the bug.\r\n#\r\n```\r\n\r\nHere it is only using 1 core I am assuming. "}}
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