Question: galaxy_filter_sam report error
0
gravatar for garentguuu
7 months ago by
garentguuu10
garentguuu10 wrote:

Hi,

Recently, I try to use samtools: Filter SAM or BAM, output SAM or BAM, but it reported that:

#############################
 Set it manually or retry auto-detection
[E::hts_idx_push] Chromosome blocks not continuous
##############################

I don't know what is wrong with it? Any help?

Thanks, Garen

picard sort galaxy samtools bam • 263 views
ADD COMMENTlink modified 6 months ago • written 7 months ago by garentguuu10
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Did you try coordinate sorting the input BAM dataset first? That will probably resolve the problem, assuming that the BAM dataset is formatted correctly (header intact and reported alignments are present).

Support FAQs: https://galaxyproject.org/support/

If that does not work, and you can reproduce the problem at Galaxy Main, a bug report can be sent in. We are testing the pre-release of Galaxy 18.05 and would very much like to learn about new problems. Be sure to leave all inputs and the error dataset active (not deleted).

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
0
gravatar for garentguuu
6 months ago by
garentguuu10
garentguuu10 wrote:

Thanks for you help. After I sorted the bam, it works well.

Thank you! Garen

ADD COMMENTlink written 6 months ago by garentguuu10
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