Hello everyone, I’m experiencing difficulties processing the Mitos2 tools. "The server was unable to process your request. Please review your parameter settings, attempt to resubmit, and reach out to the Galaxy Team if the issue continues. Below is a record of the data you submitted, like
{
“history_id”: “ae41fb830e4d2453”,
“tool_id”: “toolshed.g2.bx.psu.edu/repos/iuc/mitos2/mitos2/2.1.9+galaxy0”,
“tool_version”: “2.1.9+galaxy0”,
“inputs”: {
“input”: {
“batch”: false,
“product”: false,
“values”: [
{
“id”: “26c75dcccb616ac8aed09c128a8a92dc”,
“src”: “hda”,
“map_over_type”: null
}
]
},
“code”: “2”,
“refseqver”: “refseq63m”,
“linear”: false,
“addoutputs”: [
“fas”
],
“advanced|featuretypes”: [
“prot”,
“trna”,
“rrna”
],
“advanced|finovl”: “50”,
“advanced|best”: false,
“advanced|fragovl”: “20”,
“advanced|fragfac”: “10.0”,
“advanced_prot|evalue”: “2.0”,
“advanced_prot|cutoff”: “50”,
“advanced_prot|clipfac”: “10.0”,
“advanced_prot|ncbicode”: false,
“advanced_prot|alarab”: false,
“advanced_prot|oldstst”: false,
“advanced_ncrna|locandgloc”: false,
“advanced_ncrna|ncev”: “0.01”,
“advanced_ncrna|sensitive”: false,
“advanced_ncrna|maxtrnaovl”: “50”,
“advanced_ncrna|maxrrnaovl”: “50”
}
}
Please help me and let me know the solution. Thank you.
Maybe share the history, so, people can check what is going on. If you have many datasets, copy input data into a new history and submit the job.
To share a history, click at History options (three horizontal bars icon) in the top right corner > Share and manage access > Make history accessible (in the middle window), copy and paste the link into reply.
Kind regards,
Igor
thank you for your respond, this the link my project
Thanks for sharing the history as @igor suggested. Very helpful!
And I can see that you have tried the prior help from here (standardizing the fasta format) → MITOS2 error can't run job
I can also see the warning on the Mitos2 tool form when selecting the different fasta formatted datasets in your history. For you and anyone running into this issue later on, it will look something like this. A bit confusing with the programming logic exposed, but whenever the Run Tool button has a hover-over message, this indicates a data conflict issue that needs to be resolved (or, expect problems!) with any tool.
From what I can tell, the problem is that while these inputs are in the correct format there is still a conflict with the content of the files. Mitos2 is expecting an input with a single fasta sequence record. Your datasets contain fasta datasets with multiple records. How to check? Inspect using the eye icon for small datasets, or run a tool like Fasta Statistics and review the report.
Help
MITOS2 does a de-novo annotation of a given metazoan mitochondrial sequence.
Inputs
- A fasta formatted sequence
- MITOS2 processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool Split Fasta files into a collection. The resulting collection can then used as input to MITOS2.
- The correct genetic code needs to be selected
- Reference data needs to be selected (can be provided by an administrator using the MITOS data manager)
I would try running Collection Operations → Split Fasta files into a collection on your file. You can then run Mitos2 on the entire collection as a batch.
Please give that a try and let us know what happens! If you still have problems, a screenshot of the tool form filled out with your input choices (input dataset and other parameters) will help with more troubleshooting. Thanks! 
First of all, thank you for your help. So, it means I need to split the FASTA file that I have first and then run MITOS. I’m still unsure about how we can identify the mitochondrial sequence—does it mean we directly use the BLAST results, split them, and then run MITOS, or how?
Glad that helped!
For your question about pre-processing, from what I understand, this is the tool that is doing the search/find for you. The mitochondrial genome might be split across different contigs. Mitos2 will aid in identifying and annotating them. So, splitting what you have then running Mitos2 is the core workflow.
The output by default is a BED file. You could merge these together, filter based on your own criteria, then use that to perform any downstream steps.
- Collapse Collection into single dataset in order of the collection
- More help for data manipulation tools can be found at the
GTN site. These are good places to start, but please ask if you can’t find something and need a extra tips!
- GTN Materials Search (query=olympics)
- GTN Materials Search (query=collection)
The Mitos2 tool help site linked on the tool form includes a video of the core steps for both Galaxy and command line along with a link to the tool’s publication. It was the prior site of the web hosted tool but was updated to reflect the new usage options.
I hope this also helps but please let us know if it actually does! 