PositionalAssembler Error: Invalid file pointer #694
Description
Dear developers of GRIDSS,
Thank you for your effort in keeping the tool updated for so many years. I'm trying making a PoN from 2 samples just for testing purposes. I manage setting up the reference and creating the VCF file from the starting BAM for on one of the 2 files but on the second one i got:
PositionalAssembler Error during assembly of chromosome chr6 (262 reads in graph). Attempting recovery by rebuilding assembly graph. htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Invalid file pointer: 708882317835559 for FILE at htsjdk.samtools.BAMFileReader$BAMFileIterator.readNextRecord(BAMFileReader.java:972) at htsjdk.samtools.BAMFileReader$BAMFileIterator.access$1800(BAMFileReader.java:804) at htsjdk.samtools.BAMFileReader$BAMFileIterator$AsyncBamDecoder.performReadAhead(BAMFileReader.java:932) at htsjdk.samtools.util.AsyncReadTaskRunner.readNextBatch(AsyncReadTaskRunner.java:226) at htsjdk.samtools.util.AsyncReadTaskRunner.lambda$scheduleFutures$2(AsyncReadTaskRunner.java:206) at java.base/java.util.concurrent.CompletableFuture$UniApply.tryFire(CompletableFuture.java:642) at java.base/java.util.concurrent.CompletableFuture$Completion.run(CompletableFuture.java:478) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) Caused by: java.io.IOException: Invalid file pointer: 708882317835559
I'm attaching the gridss_minimal_reproduction_data_for_error_1.zip file
Thank you for your help!