Error when sorting bam file for query name using Picard

Question: Error when sorting bam file for query name using Picard

3.4 years ago by

jei2032 • 0

United States

jei2032 • 0 wrote:

Hi, I am new to data analysis and so far I have been able to navigate Galaxy - thanks for making this available!!!

I am trying to sort a filtered BAM file by query name (its paired end data) using Picard and I get the following error:

48 SortSam on data 15: BAM sorted in queryname order

2.1 GB

formatbam

database?

[bam_index_core] the alignment is not sorted (D7ZQJ5M1_744:8:1101:10000:10609): 64920643 > 64920521 in 16-th chr [bam_index_build2] fail to index the BAM file. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch *** glibc detected *** pyt

I have tried to decipher the message but I don't understand the error. The bam files were originally sorted by coordinates so I know it should be possible to sort.

Help please!

Thanks!!

galaxy picard bam • 1.4k views

ADD COMMENT • link •

modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by jei2032 • 0

The bam file I am trying to sort is already sorted by coordinate. Could the problem be due to re-sorting?

ADD REPLY • link written 3.4 years ago by jei2032 • 0

Hello, I can replicate this problem on http://usegalaxy.org. We will investigate and get back to you. Thanks for reporting the issue. Jen, Galaxy team

ADD REPLY • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This issue is still open. We were waiting to see if the recent code updates would resolve the problems, but fresh tests show that any fixes made have not yet been applied to http://usegalaxy.org. Please follow this Trello ticket for updates going forward: https://trello.com/c/lwAdo5NG

Sorry for the inconvenience and thank you again for reporting the problem! Jen, Galaxy team

ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi,

Damion here at British Columbia CDC. I think we ran into the same problem last week. So thanks for pursuing a solution here.

ADD REPLY • link written 3.2 years ago by damiondooley • 0

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