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...
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
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
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
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