unicycler input files

Question: unicycler input files

15 months ago by

repizo • 0

repizo • 0 wrote:

hi, I am trying to assemble a plasmid using unicycler. I have illumina reads (single) in fastq.gz format (48 files). It seems that unicycler only allows fastqsanger reads as input. I tried converting my reads. I tried converting my files to .fastqsanger but there still not recognized by unicycler. I would appreciate any help, first time using Galaxy...

unicycler • 579 views

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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by repizo • 0

15 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update 2017-08-29

The tool has been confirmed to have a configuration issue. All jobs are resulting in a server error. This means that the changes for format are not a factor that will fix usage problems (yet). All can follow here for the correction: https://github.com/galaxyproject/galaxy/issues/4516

Thanks for reporting the problem! The issue is new and appears to have been introduced within the last week or so.

Jen, Galaxy team

ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

15 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the tool expects fastqsanger formatted input and for that datatype to be assigned. Please see the first two FAQ links here for how to prep fastq data: https://galaxyproject.org/support/#getting-inputs-right-

I see that your data has the datatype fastqcssanger.gz assigned to uncompressed fastq data. That will not be recognized and the assignment was likely a small mistake when you intended to assign fastqsanger.gz. However, because the data is uncompressed, use fastqsanger instead.

In short, the datatype for uncompressed fastq data should be fastqsanger. The datatype for compressed fastq data should be fastqsanger.gz. The tool may launch and begin to run even when the actual content versus the assigned datatype is mixed up, but the job will eventually error.

Hope this helps! Jen, Galaxy

ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

15 months ago by

repizo • 0

repizo • 0 wrote:

Actually I uploaded fastq.gz data. Unless it changed during the uploading process, it should have remained that way. Am I right? thanks

ADD COMMENT • link written 15 months ago by repizo • 0

It appears that the uploaded data was uncompressed during that processing. To retain compressed data and have that loaded into your history, assign the compressed datatype in the Upload tool (instead of using autodetect).

ADD REPLY • link modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson ♦ 25k

15 months ago by

repizo • 0

repizo • 0 wrote:

Hi Jennifer, I succeeded converting my fastq files into fastqsanger. Now I would need to combine all these small files into one, in order to launch unicycler. I couldn't find a way to do that from the history panel. could you please help me with that? thanks

ADD COMMENT • link written 15 months ago by repizo • 0

Use the tool Text Manipulation > Concatenate to combine fastq data.

ADD REPLY • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

15 months ago by

repizo • 0

repizo • 0 wrote:

I got this error when running unicycler

Remote job server indicated a problem running or monitoring this job.

ADD COMMENT • link written 15 months ago by repizo • 0

Hello -

The new set of inputs are now in compressed fastq format (fastq.gz). I noticed that you changed the last two to have the datatype fastqsanger. That would be a mismatch for the type and should be fastqsanger.gz (if a change is needed at all - it depends on the downstream tool).

To fix the tool error, it might be enough to just change the Collapse Collection result dataset to have the datatype fastqsanger.gz and then run Unicycler again. Collapse Collection accepts fastq.gz datatype input directly and is another valid tool for combining datasets.

If that run is problematic, you may need to go back further and reprocess some steps. The inputs to Collapse Collection did not all have the same datatype. The two changed to fastqsanger could be changed back to fastq.gz and Collapse Collection run again, the datatype fastqsanger.gz assigned, and then run Unicycler.

Thanks! Jen

ADD REPLY • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

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