csi indexing of *.bam.sv.bam - invalid file pointer #520
Description
I'm finding that the csi index generated for the *.bam.sv.bam file in some instances results in an invalid file pointer:
INFO 2021-08-17 07:24:30 AssemblyEvidenceSource Starting assembly on chunk 164 (9:98840289-9:108840288)
ERROR 2021-08-17 07:24:31 AssemblyEvidenceSource Error assembling chunk 164 (9:98840289-9:108840288)
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Invalid file pointer: 686201611812555 for /var/spool/workspace/PD13371b.sample.dupmarked.bam.gridss.working/PD13371b.sample.dupmarked.bam.sv.bam
at htsjdk.samtools.BAMFileReader$BAMFileIterator.readNextRecord(BAMFileReader.java:972)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.access$1800(BAMFileReader.java:804)
at htsjdk.samtools.BAMFileReader$BAMFileIterator$AsyncBamDecoder.performReadAhead(BAMFileReader.java:932)
at htsjdk.samtools.util.AsyncReadTaskRunner.readNextBatch(AsyncReadTaskRunner.java:226)
at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1700)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.io.IOException: Invalid file pointer: 686201611812555 for /var/spool/workspace/PD13371b.sample.dupmarked.bam.gridss.working/PD13371b.sample.dupmarked.bam.sv.bam
at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:382)
at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.advanceToNextRecordStart(BAMFileReader.java:1136)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.readNextRecord(BAMFileReader.java:952)
... 7 more
Rerunning gives the same result, however if I reindex the file with the 1.10 samtools included in the docker image the processing can be resumed.
Under GRCh38 this works fine, but GRCh37 it fails on the same sample. Just logging here incase others encounter this.
Example command:
gridss \
--steps preprocess,assemble,call \
--externalaligner \
--reference ref/genome.fa \
--blacklist ref/gridss/blacklist-2011-05-04-ENCFF001TDO.bed \
--threads 8 \
--labels SAMPLE \
--skipsoftcliprealignment \
--assembly result/PD13371b.assembly.bam \
--output result/SAMPLE.gridss.vcf.gz \
--workingdir workspace \
SAMPLE.sample.dupmarked.bam