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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Error running gridss_annotate_vcf_repeatmasker from docker image #535

Closed tea-kostic closed 2 years ago

tea-kostic commented 3 years ago

Hi,

When running gridss_annotate_vcf_repeatmasker from gridss/gridss:2.12.2 on AWS cloud, I get the following error:

Mon Oct 18 09:46:45 UTC 2021: Using 8 worker threads.
Mon Oct 18 09:46:45 UTC 2021: Found /opt/RepeatMasker/RepeatMasker
Mon Oct 18 09:46:45 UTC 2021: Found /usr/bin/java
Mon Oct 18 09:46:45 UTC 2021: RepeatMasker version: RepeatMasker version 4.1.2-p1
Mon Oct 18 09:46:45 UTC 2021: bash version: GNU bash, version 5.0.17(1)-release (x86_64-pc-linux-gnu)
Mon Oct 18 09:46:45 UTC 2021: java version: openjdk version "11.0.11" 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)
09:46:46.168 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gridss/gridss-2.12.2-gridss-jar-with-dependencies.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Oct 18 09:46:46 UTC 2021] InsertedSequencesToFasta --INPUT sample.gridss.unfiltered.vcf.gz --OUTPUT ./sample.gridss.unfiltered.vcf.gz.fa --MIN_SEQUENCE_LENGTH 20 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 18 09:46:46 UTC 2021] Executing as root@34a3f60aaaa0 on Linux 5.4.0-1056-aws amd64; OpenJDK 64-Bit Server VM 11.0.11+9-Ubuntu-0ubuntu2.20.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.12.2-gridss
[Mon Oct 18 09:46:46 UTC 2021] gridss.InsertedSequencesToFasta done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=67108864
RepeatMasker::createLib(): Error invoking /opt/rmblast/makeblastdb on file /opt/RepeatMasker/Libraries/CONS-Dfam_3.3/general/is.lib.

How can I solve this?

Thanks, Tea

scwatts commented 3 years ago

Hi Tea, this error is caused by the Docker image missing the makeblastdb binary. I've fixed this in a Docker image our group is using as the basis for the GRIDSS/PURPLE/Linx pipeline here.

@d-cameron would you like a PR to ship this fix to the official GRIDSS Docker image?

tea-kostic commented 3 years ago

Hi Stephen, this fixed the issue, thanks a lot for your help!