Over the weekend, I tried to assemble a phage genome using Unicycler from a 150cycles Miseq data (not paired end) and an oxford nanopore run.
I keep getting the message “Remote job server indicated a problem running or monitoring this job.”. My guess is that my input files are wrong. For the illumina data, I am entering the fastq filed returned by the Miseq which galaxy recognizes as fastqsanger. The nanopore data was a bunch of different fastq files that are not recognized as fastqsanger by galaxy. I combined all the fastq files from the nanopore into one fastq file using the “Text Manipulation -> Concatenate datasets tail-to-head”. So for unicycler, I entered the one fastq from my Miseq run and the combined fastq file from the nanopore and every single time I get the error message "“Remote job server indicated a problem running or monitoring this job”.
Can someone please help me with this ? I am new with all these tools.