gridss call error

[vitty0513]

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

the log is : [M::process] read 107586 sequences (10000251 bp)... [M::mem_process_seqs] Processed 107586 reads in 128.060 CPU sec, 77.282 real sec [M::process] read 109438 sequences (10000015 bp)... [M::mem_process_seqs] Processed 109438 reads in 130.298 CPU sec, 78.896 real sec [M::process] read 107308 sequences (10000062 bp)... [M::mem_process_seqs] Processed 107308 reads in 134.199 CPU sec, 81.460 real sec [M::process] read 109800 sequences (10000000 bp)... [M::mem_process_seqs] Processed 109800 reads in 119.501 CPU sec, 72.211 real sec INFO 2023-06-11 13:44:43 AnnotateInsertedSequence Processed 17,000,000 records. Elapsed time: 06:02:54s. Time for last 1,000,000: 1,206s. Last read position: LG30:6,448,011 [M::process] read 108234 sequences (10000158 bp)... [M::mem_process_seqs] Processed 108234 reads in 123.077 CPU sec, 74.206 real sec [M::process] read 107940 sequences (10000061 bp)... [M::mem_process_seqs] Processed 107940 reads in 122.843 CPU sec, 74.315 real sec INFO 2023-06-11 13:53:50 ExternalProcessStreamingAligner Waiting for external aligner to complete all alignments. [M::process] read 27311 sequences (2554035 bp)... [M::mem_process_seqs] Processed 27311 reads in 32.186 CPU sec, 19.362 real sec ERROR 2023-06-11 13:54:50 ExternalProcessHelper External process still alive: "bwa mem -K 10000000 -L 0,0 -t 8 /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa -" ERROR 2023-06-11 13:54:50 ExternalProcessHelper Subprocess terminated with with exit status 137. Failed executing "bwa mem -K 10000000 -L 0,0 -t 8 /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa -". Can you run the alignment command from the command line? Is the aligner on PATH? Did you build an index with prefix /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa? Exception in thread "feedAligner" java.lang.RuntimeException: Subprocess terminated with with exit status 137. Failed executing "bwa mem -K 10000000 -L 0,0 -t 8 /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa -". Can you run the alignment command from the command line? Is the aligner on PATH? Did you build an index with prefix /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa? at au.edu.wehi.idsv.alignment.ExternalProcessHelper.shutdown(ExternalProcessHelper.java:40) at au.edu.wehi.idsv.alignment.ExternalProcessHelper.shutdownAligner(ExternalProcessHelper.java:44) at au.edu.wehi.idsv.alignment.ExternalProcessStreamingAligner.flush(ExternalProcessStreamingAligner.java:103) at au.edu.wehi.idsv.alignment.StreamingAlignerIterator.flush(StreamingAlignerIterator.java:31) at au.edu.wehi.idsv.vcf.InsertedSequenceAnnotator.feedStreamingAligner(InsertedSequenceAnnotator.java:110) at au.edu.wehi.idsv.vcf.InsertedSequenceAnnotator.lambda$new$0(InsertedSequenceAnnotator.java:48) at java.lang.Thread.run(Thread.java:748) Exception in thread "ExternalProcessStreamingAligner" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed at htsjdk.samtools.util.BufferedLineReader.readLine(BufferedLineReader.java:70) at htsjdk.samtools.SAMTextReader.advanceLine(SAMTextReader.java:221) at htsjdk.samtools.SAMTextReader.access$800(SAMTextReader.java:37) at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:257) at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:228) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:574) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:553) at au.edu.wehi.idsv.alignment.ExternalProcessStreamingAligner.readAllAlignments(ExternalProcessStreamingAligner.java:139) at au.edu.wehi.idsv.alignment.ExternalProcessStreamingAligner.lambda$ensureAligner$2(ExternalProcessStreamingAligner.java:77) at java.lang.Thread.run(Thread.java:748) Caused by: java.io.IOException: Stream closed at java.io.BufferedInputStream.getBufIfOpen(BufferedInputStream.java:170) at java.io.BufferedInputStream.read(BufferedInputStream.java:336) at java.io.BufferedInputStream.fill(BufferedInputStream.java:246) at java.io.BufferedInputStream.read1(BufferedInputStream.java:286) at java.io.BufferedInputStream.read(BufferedInputStream.java:345) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.LineNumberReader.readLine(LineNumberReader.java:201) at htsjdk.samtools.util.BufferedLineReader.readLine(BufferedLineReader.java:68) ... 9 more

However I have built an index. How can I solve this error?

Many thanks

[vitty0513]

I have module load BWA/0.7.17 and there're indexes: Lachesis_assembly_changed.dict Lachesis_assembly_changed.fa Lachesis_assembly_changed.fa.amb Lachesis_assembly_changed.fa.ann Lachesis_assembly_changed.fa.bwt Lachesis_assembly_changed.fa.fai Lachesis_assembly_changed.fa.pac Lachesis_assembly_changed.fa.sa

I don't find anything wrong with my reference genome index and the PATH. It's very strange!

[d-cameron]

ERROR 2023-06-11 13:54:50 ExternalProcessHelper Subprocess terminated with with exit status 137. Failed executing "bwa mem -K 10000000 -L 0,0 -t 8 /home/banliping/WORKSPACE/dwt/ACB/ref/Lachesis_assembly_changed.fa -". Can you run the alignment command from the command line? Is the aligner on PATH? Did you build an index with prefix

What happens when you try to run the quoted command from the command line?