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I checked this issue because I ran into the same p...
# sarek_dev
f
I checked this issue because I ran into the same problem now for a bigger dataset: https://github.com/nf-core/sarek/issues/2166
r
If there is no usable adta in the table, maybe sharding less would help?
f
how would I control that? 🤔
r
playing around with nucleotides_per_second
👍 1
increasing it reduced the number of shards
f
perfect I will try and comment on the issue
I changed up to 800000 and also tried it without my custom bed, the error persists
I think this is rather related to an actual bug that we introduce somewhere 🤔
r
is there anything more interesting in the logs? I am asking becaus ewe don't see it persistently
f
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12:03:25.388 INFO  GatherBQSRReports - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  12:03:25.388 INFO  GatherBQSRReports - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  12:03:25.388 INFO  GatherBQSRReports - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  12:03:25.389 INFO  GatherBQSRReports - Deflater: IntelDeflater
  12:03:25.389 INFO  GatherBQSRReports - Inflater: IntelInflater
  12:03:25.389 INFO  GatherBQSRReports - GCS max retries/reopens: 20
  12:03:25.389 INFO  GatherBQSRReports - Requester pays: disabled
  12:03:25.390 INFO  GatherBQSRReports - Initializing engine
  12:03:25.390 INFO  GatherBQSRReports - Done initializing engine
  12:03:25.591 INFO  GatherBQSRReports - Shutting down engine
  [May 15, 2026 at 12:03:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports done. Elapsed time: 0.01 minutes.
  Runtime.totalMemory()=92274688
  org.broadinstitute.hellbender.exceptions.GATKException: there is no usable data in any input file
        at org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.lambda$gatherReports$2(RecalibrationReport.java:119)
        at java.base/java.util.Optional.orElseThrow(Optional.java:403)
        at org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.gatherReports(RecalibrationReport.java:119)
        at org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.gatherReportsIntoOneFile(RecalibrationReport.java:85)
        at org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports.doWork(GatherBQSRReports.java:37)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)

Work dir:
  /mnt/lustre/groups/nahnsen/nahbu450/japan/work/8d/380799bd03d31ce1338c397ee7c657

Container:
  /mnt/lustre/groups/nahnsen/nahbu450/japan/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-b2-b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98-data.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
Join mismatch for the following entries:
- key=[patient:HG03464, sample:HG03464, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG03464] values=
- key=[patient:HG02012, sample:HG02012, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG02012] values=
- key=[patient:HG01049, sample:HG01049, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG01049] values=
- key=[patient:HG03224, sample:HG03224, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG03224] values=
- key=[patient:HG02256, sample:HG02256, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG02256] values=
- key=[patient:HG03460, sample:HG03460, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG03460] values=
- key=[patient:HG03342, sample:HG03342, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG03342] values=
- key=[patient:HG01284, sample:HG01284, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG01284] values=
- key=[patient:HG02130, sample:HG02130, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG02130] values=
- key=[patient:HG03583, sample:HG03583, sex:NA, status:0, n_fastq:12, data_type:cram, id:HG03583] values=
(more omitted)
there is this weird join mismatch which shows up
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