BAM files fail to be recognized

Question: BAM files fail to be recognized

19 months ago by

deepti1rao • 10 wrote:

I generated BAM files on galaxy using BWA-MEM. I am trying to run BAMtools, Picard, etc on them. But none of them work.

I got this error when I tried inputting one file at a time:

open: No such file or directory [bam_index_build2] fail to open the BAM file. Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/689/15689525/_galaxy_tmp -Xmx7680m -Xms256m

When I tried inputting multiple files, galaxy asked to "Verify this parameter". i.e. Input SAM/ BAM files.

galaxy bam • 570 views

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modified 19 months ago by y.hoogstrate • 460 • written 19 months ago by deepti1rao • 10

19 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

What happens if you reset the metadata on the BAM datasets (this will ensure the .bam.bai index is available)? Do this by clicking on the pencil icon to reach the edit attribute forms. Assigning the database is also a good idea and can be done on the same set of forms. I am assuming that the datatype "BAM" has already been set by BWA-MEM.

You will also want to coordinate sort the BAM files before using them with other tools, especially those in the Picard or SAMtools groups. SortSAM is one option (accepts BAM or SAM input).

If you cannot determine the problem, please send in a bug report. Make sure the inputs and error datasets are undeleted. We can review and offer advice. Please include a link to this Biostars post in the comments.

Sorry you are having trouble, Jen, Galaxy team

ADD COMMENT • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

deepti1rao • 10

deepti1rao • 10 wrote:

My problem has not resolved yet.

I was trying to convert BAM files (10,11,12) into SAM files. It didn't work.

I even converted them into BAI using convert format by clicking on the pencil icon. However, I couldn't execute SAMtools even after that.

What am I doing wrong?

Here's the link to my history:

https://usegalaxy.org/u/dazzlingdee/h/galaxy-project

ADD COMMENT • link written 19 months ago by deepti1rao • 10

19 months ago by

y.hoogstrate • 460

Netherlands

y.hoogstrate • 460 wrote:

Those are SAM files, not BAM files. Can you convert (revert?) them with 'SAM-to-BAM convert SAM to BAM' and see if that works out for you?

ADD COMMENT • link modified 19 months ago • written 19 months ago by y.hoogstrate • 460

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