Deterioration of IlluminaBasecallsToSam performance and memory usage over the past year

[alecw]

Bug Report

Affected tool(s)

IlluminaBasecallsToSam

Affected version(s)

• 2.25.0 .. 2.26.2

Description

IlluminaBasecallsToSam has gotten slower and memory use has increased in releases over the past year.

Steps to reproduce

I ran a small job on various versions of picard:
java -Djava.io.tmpdir=/broad/hptmp/alecw/HFNTVAFX3 -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx29384m -jar picard.jar IlluminaBasecallsToSam TMP_DIR=/broad/hptmp/alecw/HFNTVAFX3 VALIDATION_STRINGENCY=SILENT BASECALLS_DIR=/broad/mccarroll/dropulation_census/raw_data/2022-01-04/225552339/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HFNTVAFX3 NUM_PROCESSORS=1 READ_STRUCTURE=83T83T INCLUDE_NON_PF_READS=false APPLY_EAMSS_FILTER=false MAX_RECORDS_IN_RAM=600000 IGNORE_UNEXPECTED_BARCODES=false SEQUENCING_CENTER=BI OUTPUT=test.bam SAMPLE_ALIAS=xxx LIBRARY_NAME=xxx ADAPTERS_TO_CHECK=null RUN_START_DATE=01/04/2022

Expected behavior

_Successful completion in ~15 minutes.

Actual behavior

• 2.24.2: succeeds in 15 minutes
• 2.25.0: succeeds in 31 minutes
• 2.25.6: runs out of memory
• 2.26.0: runs out of memory
• 2.26.10: runs out of memory

Let me know if you'd like me to try other versions, or if there is anything else I can do.

[gbggrant]

Thanks @alecw for this summary of the performance degradation. We have also seen some significant performance degradation for some of these tools.

The degradation may be due to some pull requests that have been contributed to Picard. @tfenne @jacarey do you have any input here?

[jacarey]

@gbggrant I'm happy to take a look. Would it be possible to share this data with me as a test set?

[gbggrant]

@alecw - to you - is it okay to share this data set with @jacarey ?

[alecw]

Run folder is 21G. Where should I copy it so that Jay can access?

[alecw]

@gbggrant , @jacarey waiting to hear from you

[gbggrant]

@jacarey have you been able to look at the data that was sent along for this?