ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 1-15215340, Mate Alignment start should be 0 because reference name = *

[kuangzhuoran]

My command is "gridss -r ref.fa -j ./gridss-2.13.2-gridss-jar-with-dependencies.jar -o test.vcf A1.bam"

The corresponding line in the bam file looks like this:
1-15215340 81 chr1 11538 30 150M * 14314113 0 ......

My idea was to remove the seventh column of the line with the “*”

Here are the log:
[Fri Aug 30 17:41:21 CST 2024] Executing as kuangzhuoran@cu08 on Linux 3.10.0-1127.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.13.2-gridss
[Fri Aug 30 17:41:24 CST 2024] gridss.analysis.CollectGridssMetrics done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2147483648
Exception in thread "main" java.lang.RuntimeException: htsjdk.samtools.SAMFormatException: SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 1-15215340, Mate Alignment start should be 0 because reference name = *.
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:253)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:134)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:126)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:598)
at gridss.analysis.CollectGridssMetrics.doWork(CollectGridssMetrics.java:78)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:196)
at gridss.analysis.CollectGridssMetrics.main(CollectGridssMetrics.java:55)
Caused by: htsjdk.samtools.SAMFormatException: SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 1-15215340, Mate Alignment start should be 0 because reference name = *.
at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:447)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.decode(BAMFileReader.java:896)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.access$1900(BAMFileReader.java:804)
at htsjdk.samtools.BAMFileReader$BAMFileIterator$AsyncBamDecoder.transform(BAMFileReader.java:942)
at htsjdk.samtools.BAMFileReader$BAMFileIterator$AsyncBamDecoder.transform(BAMFileReader.java:925)
at htsjdk.samtools.util.AsyncReadTaskRunner.processNextBatch(AsyncReadTaskRunner.java:257)
at java.base/java.util.concurrent.CompletableFuture$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)