I have not been able to get Salmon to work for the past four days. Following the instructions of a previous post, I deleted the old jobs and I have been starting new ones for the past few days but they remain on queue and do not progress.
Yes, it worked fine before. The job would be completed in a few hours.
Yes, I tried it with the test dataset and as you mentioned, it worked fine in a few minutes with the same results. I do think the problem is that my files are too large. The reference transcriptome is Xenopus (2.6GB) and my transcriptome from Trinity is 295.9 MB. Is there a different route that is recommended to quantify the transcriptome from Trinity?
Yes, how do I go about splitting the file into two? Thank you.
1run 'FASTA-to-Tabular' on the ref file.
2 use 'Select first ' on the output to select as many sequences as you want in the file
3 on this output run 'Tabular-to-FASTA '
This should give you a smaller file.
If you want to select lines not starting at the beginning of the file you can use a sequential combination of 'Select last', 'Select first ' and 'Remove beginning ' the following tools at step 2 (not in any particular order here )
Was the tool working for you before?are you using usegalaxy.org?
I just tried the tool on use galaxy.org just now with the test datasets given on the program homepage salmon.It worked fine for me. Finished in a few seconds and output looks good.
Here is the history I have shared it publicly and through the link https://usegalaxy.org/u/guy1/h/salmon-test-dataset
I think you may need to look into the possibility that there is something wrong with your files or they are too large.
Try running the test yourself Cheers
Guy Ps I may have been better if you responded to my question as a 'comment' and not as a 'reply' as doing this makes it look like your issue has been resolved when I do not think it yet has. Maybe you can delete your reply and put if in as a comment - if that is possible. This maximises your chances of getting help.