Question: Bedgraph to bigwig generates error
1
gravatar for djevo1
5 months ago by
djevo150
djevo150 wrote:

I am running bedgraph to bigwig on a local galaxy and am receiving this error. The bedgraph files are set to the correct genome build and the .len file has been created.

Fatal error: Matched on Error
Error running wigToBigWig.
rna-seq bedgraph bigwig • 246 views
ADD COMMENTlink written 5 months ago by djevo150

There is likely an admin configuration error, if you are certain the genomes are an exact match and the genome fasta itself has been added to the local and indexed for SAMtools, Picard, and 2bit (recommended for all genomes to be used as a baseline, add in other indexes as wanted).

There could be other related factors (job uses more resources than available on the local - specifically memory), but the test below can help determine that and help with further troubleshooting.

One way to test is to see if the jobs work at http://usegalaxy.org. Use a Custom reference genome "Build" if needed. A custom genome build could also be used on your local, but less resources will be used if installed/indexed.

Thanks, Jen, Galaxy team

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson22k

I used the db keys all fasta to generate the len file, inedexed for picard, samtools, 2bit. I may know what it is however. Is there a way to generate a len file from multiple fasta files, one for each chromosome?

ADD REPLYlink written 5 months ago by djevo150

Finally got around to uploading the len file to usegalaxy, I receive the same error. I was using one of my bam files as well.

hashMustFindVal: 'GL000192.1' not found

ADD REPLYlink written 5 months ago by djevo150
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

Yes, you can load individual chromosome fasta files as distinct "reference genomes" and index from there. Use the same Data Manger. Load the fasta for each and choose the source as "from the history".

  • Make sure each dbkey is distinct
  • Make sure that the title line for each chromosome fasta file has a unique identifier and that there is no description content. https://wiki.galaxyproject.org/Learn/Datatypes#Fasta
  • Wrap the fasta lines to a consistent length (40-80 bases)
  • Build the indexes in this order: Load fasta (allow to complete), Samtools (allow to complete), Picard (allow to complete), 2bit and any others can be run concurrently after, if your server has the resources. Otherwise just run one at a time.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson22k

Finally got around to uploading the len file to usegalaxy, I receive the same error. I was using one of my bam files as well.

hashMustFindVal: 'GL000192.1' not found

ADD REPLYlink written 5 months ago by djevo150
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