Question: Error when sorting bam file for query name using Picard
gravatar for jei2032
3.4 years ago by
United States
jei20320 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



[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: *** 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!



galaxy picard bam • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by jei20320

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

ADD REPLYlink written 3.4 years ago by jei20320

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

ADD REPLYlink written 3.4 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 Please follow this Trello ticket for updates going forward:

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

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k


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

ADD REPLYlink written 3.2 years ago by damiondooley0
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