watchdir is deprecated in minkNow 1.4.3 #3
Description
Hi Matt,
Using aReadUntil is no longer compatible with how fast5 files are generated in online mode.
Indeed the option WATCHDIR (-w) allows to indicate the directory where the reads (fast5) are. Hence their analysis is done (counting the number of 2D reads, moving reads associated to a known amplicon).
In the "new" version of MinKnow (1.4.3), reads are moved in subdirectories. This is not allowed by the ReadUntil scripts.
$/opt/ONT/MinKNOW$ ls /var/lib/MinKNOW/data/reads/
0 100 103 106 109 111 14 17 2 22 25 28 30 33 36 39 41 44 47 5 52 55 58 60 63 66 69 71 74 77 8 82 85 88 90 93 96 99
1 101 104 107 11 12 15 18 20 23 26 29 31 34 37 4 42 45 48 50 53 56 59 61 64 67 7 72 75 78 80 83 86 89 91 94 97 tmp
10 102 105 108 110 13 16 19 21 24 27 3 32 35 38 40 43 46 49 51 54 57 6 62 65 68 70 73 76 79 81 84 87 9 92 95 98
I have no idea of the meaning of each subdirectory.
We tried to put the "Recursive = True" option on reading reads in aReadUntil but this does not change the results. Subdirectory reads are not parsed.
observer.schedule(event_handler, path=args.watchdir, recursive=True)
Martin