Hi, this is my first time reporting an issue, so I apologize if I overlook info, can’t format code correctly in this flavor of markdown, etc. I’ve submitted a bug report via the Galaxy server, but, at the risk of redundancy, wanted to ask for help here to try to get the issue resolved sooner in cas…

[image] run Unicycler always got " unicycler: command not found" -- RESOLVED at UseGalaxy.org 20230210 usegalaxy.org support run Unicycler always got “/jetstream2/scratch/main/jobs/47842391/command.sh: line 110: unicycler: command not found” I am wondering if there are so…

Hi, Thanks for reporting the problem. I was looking at your history and the inputs are Ok. Am running a quick test job to see if the problem is server side or cluster, plus looking at the input closer just to rule out format/content issues. Feedback once done

Unicycler is working fine on test data. For your failure, it was due to the input reads not being paired up. Make sure to only input matched forward/reverse reads. The tools Fastq Interlacer and De-interlacer can be used to filter out reads that are not paired. Then, try another rerun. Galaxy …

Hmm… Thanks for looking into it, but I don’t think that’s the problem. I hadn’t bothered to check that there weren’t any unpaired reads in the inputs, since they were output by Trimmomatic as the relevant paired read files, but when I put it through the Fastq Interlacer today, the tool outputs the…

The fastq datasets were of different sizes with a differing number of reads (originally). They inputs how have the same number of reads. However, the new run had the \2 reads entered for forward and \1 reads entered for reverse on the tool form. The ordering should be swapped. I rerunning your job …

[image] jennaj: However, the new run had the \2 reads entered for forward and \1 reads entered for reverse on the tool form. The ordering should be swapped. I rerunning your job that way to see what results. You could also try this now - I am expecting it to work. This did work. So, please al…

Ok, I’m running the Unicycler again with the interlaced-then-de-interlaced reads in the reverse order now, and will report back if it doesn’t work (these runs have usually taken a while to error out, in my experience). However, I still have some questions: I see now that you’re right that the de-…

Thanks for writing back. Here are the stats and I found out what the issues are around the failures. Some tools are picky about format. The testing became complex but there is a solution. Matched reads must be provided in the forward and reverse inputs (only) Those reads cannot contain internal wh…

Ok, thanks for the detailed breakdown, Jennifer. I’ll try modifying the read seq IDs and re-running on my end, and will report back if it doesn’t work. It’s too bad that the SRR files sometimes contain spaces in those IDs while a lot of tools might not be designed to tolerate them; if a Galaxy-bas…

[image] dmack33: I am curious why your earlier trick of swapping the forward and reverse read inputs worked on your end and not mine I had just mixed up the tests, had about 20 running! All finished up then I went through everything all over again to figure out the root problem. [image] d…

Dear Team, I have utilized Ion torrent based sample data in fastq format and have also performed groomer to get standard fastq information. I had started assembly with single sample still it failed. Below is the error reported. “libgomp: Thread creation failed: Resource temporarily unavailable”. …

SPAdes/Unicycler assembly failures -- Resolved

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jennaj February 10, 2023, 8:19pm 14