gridss call Exception

[vitty0513]

Dear，
I met an Exception when I run:
gridss -s call --reference $ref -a assembly.bam --output ACB_gridss --jvmheap 60g --otherjvmheap 60g
--jar /home/banliping/WORKSPACE/dwt/software/gridss-2.13.2-gridss-jar-with-dependencies.jar
$dir/AH14_MarkDup.bam
$dir/AH25_MarkDup.bam
......

And the log :
INFO 2023-06-07 09:33:43 VcfTransformCommandLineProgram Annotated variants written to ./ACB_gridss.gridss.working/ACB_gridss.allocated.vcf
[Wed Jun 07 09:33:43 CST 2023] gridss.AnnotateVariants done. Elapsed time: 3,841.94 minutes.
Runtime.totalMemory()=60362326016
Wed Jun 7 09:33:52 CST 2023: Running AnnotateInsertedSequence ACB_gridss
INFO 2023-06-07 09:33:52 Defaults Found file for property samjdk.reference_fasta: /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa
INFO 2023-06-07 09:33:52 AnnotateInsertedSequence

********** NOTE: Picard's command line syntax is changing.

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********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

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********** The command line looks like this in the new syntax:

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********** AnnotateInsertedSequence -TMP_DIR . -WORKING_DIR . -REFERENCE_SEQUENCE /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa -WORKER_THREADS 8 -INPUT ./ACB_gridss.gridss.working/ACB_gridss.allocated.vcf -OUTPUT ACB_gridss

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09:33:53.323 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/storage1/wukeliang/dwt/software/gridss-2.13.2-gridss-jar-with-dependencies.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Jun 07 09:33:53 CST 2023] AnnotateInsertedSequence WORKER_THREADS=8 INPUT=./ACB_gridss.gridss.working/ACB_gridss.allocated.vcf OUTPUT=ACB_gridss WORKING_DIR=. TMP_DIR=[.] REFERENCE_SEQUENCE=/home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa MIN_SEQUENCE_LENGTH=20 ALIGNER_COMMAND_LINE=[bwa, mem, -K, 10000000, -L, 0,0, -t, %3$d, %2$s, %1$s] ALIGNER_BATCH_SIZE=500000 ALIGNMENT=REPLACE IGNORE_DUPLICATES=true 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
[Wed Jun 07 09:33:53 CST 2023] Executing as wukeliang@node-01 on Linux 3.10.0-693.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_212-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.13.2-gridss
INFO 2023-06-07 09:33:53 AnnotateInsertedSequence Annotating inserted sequences in ./ACB_gridss.gridss.working/ACB_gridss.allocated.vcf
INFO 2023-06-07 09:33:53 AnnotateInsertedSequence Using external process alignment
INFO 2023-06-07 09:33:57 ExternalProcessStreamingAligner Starting external aligner
INFO 2023-06-07 09:33:57 ExternalProcessStreamingAligner bwa mem -K 10000000 -L 0,0 -t 8 /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa -
[Wed Jun 07 09:33:57 CST 2023] gridss.AnnotateInsertedSequence done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=2058354688
Exception in thread "main" java.lang.IllegalArgumentException: Output format type is not set, or could not be inferred from the output path. If a path was used, does it have a valid VCF extension (.vcf, .vcf.gz, .bcf)?
at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:462)
at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:415)
at gridss.AnnotateInsertedSequence.saveVcf(AnnotateInsertedSequence.java:168)
at gridss.AnnotateInsertedSequence.doWork(AnnotateInsertedSequence.java:137)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at gridss.AnnotateInsertedSequence.main(AnnotateInsertedSequence.java:67)
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 82648 sequences (10000198 bp)...
[M::process] read 72218 sequences (10000240 bp)...
[M::mem_process_seqs] Processed 82648 reads in 139.468 CPU sec, 99.266 real sec
[M::mem_process_seqs] Processed 72218 reads in 135.928 CPU sec, 68.703 real sec

Now I only get a ACB_gridss.allocated.vcf and its idx file. What can I do to solve it? It means I should change the -output ACB_gridss to ACB_gridss.vcf? And how to keep going down from here, from the ACB_gridss.allocated.vcf, because it takes me a lot of time to gain the allocated.vcf and I don't want to start again from begining

Many thanks!

[d-cameron]

OUTPUT=ACB_gridss
Output format type is not set, or could not be inferred from the output path. If a path was used, does it have a valid VCF extension (.vcf, .vcf.gz, .bcf)?
It means I should change the -output ACB_gridss to ACB_gridss.vcf?

Yes, change to a .vcf or .vcf.gz suffix. The error is because GRIDSS doesn't know if you want a .vcf a .vcf.gz or a .bcf file as your output file format.

And how to keep going down from here, from the ACB_gridss.allocated.vcf, because it takes me a lot of time to gain the allocated.vcf and I don't want to start again from begining

Just change OUTPUT=ACB_gridss to OUTPUT=ACB_gridss.vcf and rerun. As long as you don't edit/delete anything in the .gridss.working directories, GRIDSS will recognise the earlier steps have completed and only run the file step(s). In fact, unless you've specified --keepTempFiles on the command line, GRIDSS will automatically delete the .allocated.vcf file when the final VCF is generated.

[vitty0513]

Thank you! And I have changed my --output to ACB_gridss.vcf, however, it created a new directory named ACB_gridss.vcf.gridss.working and it started from beginning. Maybe I should change the old directory (ACB_gridss.gridss.working) to ACB_gridss.vcf.gridss.working and then rerun? But I have a question, the old directory has only ACB_gridss.allocated.vcf file, no other files, is it because I didn't use --keepTempFiles？ Does it mean I can't run from xxx.allocated.vcf?