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RNA type identification after graphclust analysis #72
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I am repeating an NSPDK_sparseVect process on galaxy locally installed, before I start the process I notice that the system does not recognize directly as input file in the field "gspan file" the file that I generated from the former process "fasta_to_gspan". This happened even when I ran the analysis on the other galaxy, in that case I managed to let the system recognize this file (do not remember how), even though the system reported it as hidden file (then, as I mentioned in my previous message, the analysis runs forever).The problem might rely on the generation of this file gspan file then... |
Just realized that I miss the RNAfold step...running it and see what happens... |
RNA fold gives me this error:
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I broke down my initial fasta input file (which came from the whole GTF genome) in single chromosomes...the RNA fold analysis completed successfully this time...running the next steps of GraphClust_main_3r pipeline |
I am closing this issue because I guess the problem was related with my initial big input file. When I run on shorter files everything goes smoothly. |
Hi @mavino , |
Hi @mmiladi , |
Any further thought on my last question? |
Would it be a good idea to input the cluster sequnces found by graphclust into Rfam (https://rfam.xfam.org/search?q=mana#tabview=tab1) to detect the type of RNA? |
Hi @mavino , From the error report you have posted, I suspect there should be an error with the input fasta file. I wrote you an email to look into the specific case. |
I started NSPDK_sparseVect process on Galaxy and is at its third running day. I am not sure if this is normal.
Plus its input GSPAN groups file, when locally downloaded, looks like a corrupted zip file.
My email is mariano.avino@usherbrooke.ca.
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