Methods: continuing on from yesterday using Qiime 1.7.0 VM. This includes pprospector-1.0.1 and veinna-1.8.4. Previously, the input script has been reading and writing files in the Shared_Folder which was connected to the windows desktop. On a whim, thumbnails in Nautilus were disabled, all needed files were copied to the Ubuntu desktop, and the following script was run.
check_primer_barcode_dimers.py -p AATGATACGGCGACCACCGAGATCTACACTATGGTAATTGTTCCGCAAGTNGCVACBGTNGG -P ACCATCGTCAGRTARGGRAAVA -b barcodes.txt -e DNA_parameters/dna_DM.par -o out/Results: For some reason, this worked. Perhaps the delay writing to the Shared_Folder caused a problem or perhaps the NTFS formatting of the host desktop caused permission problems for the script. But now, it works!
The script was stopped after 25 minutes. In that time, +700 files were created in the output folder most with names like
Line15_GAATACCAAGTC_primer1V86_primer1V86.px and each around 5.8kB in size. In the 25 minutes it was allowed to run, the script had progressed from Line0 to Line20. The input file, barcodes.txt, contains 1056 lines of barcodes. Back of the napkin, 1000 lines at 25 mins per 20 lines is about 20 hours. Processor usage was about 30% each on 4 cores, so additional parallelization is possible. 3 hours
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