gridss somatic SV error

[dbhayal9]

Hi,

I am running gridss for somatic SV calling from Tumor Normal samples.

command: nohup sudo docker run -i -v /home/ubuntu/newspace800/CNVSOM/hg381_22XYM:/ref -v /home/ubuntu/newspace800/CNVSOM:/bam -v /home/ubuntu/newspace800/CNVSOM:/output gridss/gridss:latest gridss -r /ref/Homo_sapiens_assembly38cleaned.fasta -j /bam/gridss-2.13.2-gridss-jar-with-dependencies.jar -a /bam/all_calls.vcf.assembly.bam -s call -o /home/ubuntu/newspace800/CNVSOM/all_calls.vcf /bam/ERR2752449_sorted.bam /bam/ERR2752450_sorted.bam -t 30 &

terminal execution summary:

Using working directory "."

Wed Jan 8 12:23:37 UTC 2025: Full log file is: ./gridss.full.20250108_122337.1339f21a6b38.1.log

Wed Jan 8 12:23:37 UTC 2025: Found /usr/bin/time

Wed Jan 8 12:23:37 UTC 2025: Using GRIDSS jar /bam/gridss-2.13.2-gridss-jar-with-dependencies.jar

Wed Jan 8 12:23:37 UTC 2025: Using reference genome "/ref/Homo_sapiens_assembly38cleaned.fasta"

Wed Jan 8 12:23:37 UTC 2025: Using output VCF /home/ubuntu/newspace800/CNVSOM/all_calls.vcf

Wed Jan 8 12:23:37 UTC 2025: Using assembly bam /bam/all_calls.vcf.assembly.bam

Wed Jan 8 12:23:37 UTC 2025: WARNING: GRIDSS scales sub-linearly at high thread count. Up to 8 threads is the recommended level of parallelism.

Wed Jan 8 12:23:37 UTC 2025: Using 30 worker threads.

Wed Jan 8 12:23:37 UTC 2025: Using no blacklist bed. The encode DAC blacklist is recommended for hg19.

Wed Jan 8 12:23:37 UTC 2025: Using JVM maximum heap size of 30g for assembly and variant calling.

Wed Jan 8 12:23:37 UTC 2025: Using input file /bam/ERR2752449_sorted.bam

Wed Jan 8 12:23:37 UTC 2025: Using input file /bam/ERR2752450_sorted.bam

Wed Jan 8 12:23:37 UTC 2025: Found /usr/bin/Rscript

Wed Jan 8 12:23:37 UTC 2025: Found /usr/local/bin/samtools

Wed Jan 8 12:23:37 UTC 2025: Found /usr/bin/java

Wed Jan 8 12:23:37 UTC 2025: Found /usr/bin/bwa

Wed Jan 8 12:23:37 UTC 2025: samtools version: 1.14+htslib-1.14

Wed Jan 8 12:23:37 UTC 2025: R version: R scripting front-end version 4.1.2 (2021-11-01)

Wed Jan 8 12:23:37 UTC 2025: bwa Version: 0.7.17-r1188

Wed Jan 8 12:23:37 UTC 2025: time version: GNU time 1.7

Wed Jan 8 12:23:37 UTC 2025: bash version: GNU bash, version 5.0.17(1)-release (x86_64-pc-linux-gnu)

Wed Jan 8 12:23:37 UTC 2025: java version: openjdk version "11.0.13" 2021-10-19 OpenJDK Runtime Environment (build 11.0.13+8-Ubuntu-0ubuntu1.20.04) OpenJDK 64-Bit Server VM (build 11.0.13+8-Ubuntu-0ubuntu1.20.04, mixed mode, sharing)

Wed Jan 8 12:23:37 UTC 2025: Max file handles: 1048576

Wed Jan 8 12:23:37 UTC 2025: Running GRIDSS steps: call,

Wed Jan 8 12:23:37 UTC 2025: Skipping pre-processing

Wed Jan 8 12:23:37 UTC 2025: Skipping assembly /bam/all_calls.vcf.assembly.bam

Wed Jan 8 12:23:37 UTC 2025: Start calling /home/ubuntu/newspace800/CNVSOM/all_calls.vcf

Wed Jan 8 12:23:37 UTC 2025: Running IdentifyVariants /home/ubuntu/newspace800/CNVSOM/all_calls.vcf

"$timecmd java -Xmx$jvmheap $jvm_args -Dgridss.output_to_temp_file=true -cp $gridss_jar gridss.IdentifyVariants TMP_DIR=$workingdir WORKING_DIR=$workingdir REFERENCE_SEQUENCE=$reference WORKER_THREADS=$threads $input_args $blacklist_arg $config_args $assembly_args OUTPUT_VCF=$prefix.unallocated.vcf $picardoptions $readpairing_args" command completed with exit code 1.

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The underlying error message can be found in ./gridss.full.20250108_122337.1339f21a6b38.1.log

There is no log file creating and its throwing an error mentioned above.
Please if anyone facing issue like this please help out me.

Thanks