Error summary: ChecksumException: Checksum error

[anjalijain22]

Hello,

Hope you're doing well!

I am processing a trio whole exome VCF with seqr's pipeline and am running into a "ChecksumException: Checksum error" (full error summary below) on the SeqrMTToESTask step of the pipeline. Have you encountered this error before and/or do you have any suggestions on how to tackle this?

Many thanks in advance for your help!

Hail version: 0.2.122-be9d88a80695
Error summary: ChecksumException: Checksum error: /input_vcfs/GRCh37/Test/xxxx.mt/rows/rows/metadata.json.gz at 22528 exp: 2104288621 got: 282958800
DEBUG: 1 running tasks, waiting for next task to finish
INFO: Informed scheduler that task   SeqrMTToESTask__seqr_reference__VARIANTS__input_vcfs_GRCh_516741895c   has status   FAILED
DEBUG: Asking scheduler for work...
DEBUG: Done
DEBUG: There are no more tasks to run at this time
DEBUG: There are 1 pending tasks possibly being run by other workers
DEBUG: There are 1 pending tasks unique to this worker
DEBUG: There are 1 pending tasks last scheduled by this worker
INFO: Worker Worker(salt=2737838620, workers=1, host=60c217d95f67, username=root, pid=109071) was stopped. Shutting down Keep-Alive thread
INFO: 
===== Luigi Execution Summary =====

Scheduled 3 tasks of which:
* 1 complete ones were encountered:
    - 1 VcfFile(filename=/input_vcfs/GRCh37/Test/xxxx.vcf.gz)
* 1 ran successfully:
    - 1 SeqrVCFToMTTask(...)
* 1 failed:
    - 1 SeqrMTToESTask(...)

This progress looks :( because there were failed tasks

===== Luigi Execution Summary =====

[hanars]

If youu have the full log file that would be helpful, however this usually happens when there is a file corruption issue. If you delete all the intermediate files and start a clean loading run from scratch does that resolve the issue?

[anjalijain22]

Hi Hana, thanks for your prompt response! Restarting the pipeline from scratch worked!