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nt -> nt + ti, cannot open 17434647.fasta #6
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Hi!, sorry for the delay, just to test some in the script, could you try to split the nt.fasta in two (or four) new files and test the script for one of them?, I'm thinking the great amount of fastas is doing an I/O error. could you try also adding Best |
I split it to 6 files and it crashes the server, perhaps due to the I/O error? |
the message are mandatory in that step, could be a next improvement suppress the message. Best |
Thanks for the response. The database is downloaded directly from NCBI's ftp server. In response to your other question, yes, I am on a cluster. Per your recommendation, I ran it locally (first splitting the large file into smaller multifastas). As part of the process, the script occasionally does not find parsefasta.awk (output below). Any idea why that might be?
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Hi!, sounds like you are not putting the script and the fasta in same directory, have them in the same directory? |
hpc@hpc:/media/box1/tb/ncbint$ bash /home/box1/Downloads/pathoscope2/pasteTaxID/pasteTaxID.bash --multifasta nt.fasta --parallelJobs 50
awk: cannot open "17434647.fasta" for output (No space left on device)
Please note that there is over 4 TB of free space available on the drive so it's not a space limitation.
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