Question: Problem using PicardTools MarkDuplicates: SortingCollection: There is not enough memory per file for buffering. Reading will be unbuffered.
0
gravatar for pengxw1990
12 days ago by
pengxw19900
China/Beijing/institute of zoogly
pengxw19900 wrote:

MarkDuplicates -I KPGP-00001.final.bam -O KPGP-00001.markdup.bam -M KPGP-00001.markdup.metrics -CREATE_INDEX true -REMOVE_DUPLICATES true -ASSUME_SORTED true -VALIDATION_STRINGENCY LENIENT -TMP_DIR /mnt/12T/tmp

OpenJDK 64-Bit Server VM 1.8.0_275-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.24.2

INFO    2021-02-23 01:53:53 MarkDuplicates  After buildSortedReadEndLists freeMemory: 49282740792; totalMemory: 49578770432; maxMemory: 49578770432
INFO    2021-02-23 01:53:53 MarkDuplicates  Will retain up to 1549336576 duplicate indices before spilling to disk.
INFO    2021-02-23 01:54:34 MarkDuplicates  Traversing read pair information and detecting duplicates.

WARNING 2021-02-23 01:57:49 SortingCollection   There is not enough memory per file for buffering. Reading will be unbuffered.**

INFO    2021-02-23 02:31:19 MarkDuplicates  Traversing fragment information and detecting duplicates.
INFO    2021-02-23 03:19:01 MarkDuplicates  Sorting list of duplicate records.
INFO    2021-02-23 03:20:05 MarkDuplicates  After generateDuplicateIndexes freeMemory: 36950789560; totalMemory: 49681006592; maxMemory: 49681006592
genome • 226 views
ADD COMMENTlink modified 12 days ago by Medhat8.9k • written 12 days ago by pengxw19900
1

You can increase memory like java -Xms10G -Xmx20G -jar /path/to/picard-tools/picard.jar MarkDuplicates.

min: 10

max: 20

ADD REPLYlink modified 12 days ago • written 12 days ago by Medhat8.9k

Thanks, I will try it.

ADD REPLYlink written 12 days ago by pengxw19900
1

This is a WARNING. You should still be able to get the output.

ADD REPLYlink written 12 days ago by GenoMax96k

Yeah, i did get a output file, but it's not complete. Thanks a lot.

ADD REPLYlink written 12 days ago by pengxw19900
1

How do you know that? Were there additional errors?

ADD REPLYlink written 12 days ago by GenoMax96k

hah, you are right! for hours later, this command started running again! might it just had a rest....

ADD REPLYlink written 12 days ago by pengxw19900
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