search

HingeAssembler / HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
http://genome.cshlp.org/content/27/5/747.full.pdf+html?sid=39918b0d-7a7d-4a12-b720-9238834902fd
Other
64 stars 9 forks source link

After filter 0 active hinges #66

Closed alimayy closed 8 years ago

alimayy commented 8 years ago

Hello again,

Another MinIon long-read dataset, unfortunately not public again. Read stats:

Starting nr of reads: 60566 Len: Min: 150 Max: 22639 Mean: 2682.2158 Std Dev: 2994.1440

This time I can only make it until

hinging --db org_8 --las org_8.las -x org_8 --config ~/packages/HINGE/utils/nominal.ini -o org_8

After which I am left with no sequences to work with, I think. Should I change a parameter perhaps? Here's the log.

[2016-09-08 11:09:45.485] [log] [info] Hinging layout [2016-09-08 11:09:45.485] [log] [info] name of db: org_8, name of .las file org_8.las [2016-09-08 11:09:45.486] [log] [info] name of fasta: , name of .paf file [2016-09-08 11:09:45.486] [log] [info] filter files prefix: org_8 [2016-09-08 11:09:45.486] [log] [info] output prefix: org_8 [2016-09-08 11:09:45.506] [log] [info] Parameters passed in

[2016-09-08 11:09:45.557] [log] [info] Load alignments from org_8.las [2016-09-08 11:09:45.557] [log] [info] # Alignments: 958702 [2016-09-08 11:09:45.557] [log] [info] # Reads: 48830 [2016-09-08 11:09:47.660] [log] [info] Input data finished [2016-09-08 11:09:47.667] [log] [info] LENGTH_THRESHOLD = -1 [2016-09-08 11:09:47.667] [log] [info] QUALITY_THRESHOLD = 0 [2016-09-08 11:09:47.667] [log] [info] ALN_THRESHOLD = -1 [2016-09-08 11:09:47.667] [log] [info] MIN_COV = -1 [2016-09-08 11:09:47.667] [log] [info] CUT_OFF = -1 [2016-09-08 11:09:47.667] [log] [info] THETA = -1 [2016-09-08 11:09:47.667] [log] [info] N_ITER = -1 [2016-09-08 11:09:47.667] [log] [info] THETA2 = 0 [2016-09-08 11:09:47.667] [log] [info] N_PROC = 4 [2016-09-08 11:09:47.667] [log] [info] HINGE_SLACK = 1000 [2016-09-08 11:09:47.667] [log] [info] HINGE_TOLERANCE = 150 [2016-09-08 11:09:47.667] [log] [info] KILL_HINGE_OVERLAP_ALLOWANCE = 300 [2016-09-08 11:09:47.667] [log] [info] KILL_HINGE_INTERNAL_ALLOWANCE = 40 [2016-09-08 11:09:47.667] [log] [info] MATCHING_HINGE_SLACK = 200 [2016-09-08 11:09:47.667] [log] [info] MIN_CONNECTED_COMPONENT_SIZE = 8 [2016-09-08 11:09:47.668] [log] [info] USE_TWO_MATCHES = true [2016-09-08 11:09:47.668] [log] [info] del_telomeres = false [2016-09-08 11:09:47.699] [log] [info] read mask finished [2016-09-08 11:09:47.845] [log] [info] read marked repeats [2016-09-08 11:09:47.845] [log] [info] killed 0 reads with many repeats [2016-09-08 11:09:47.959] [log] [info] read marked hinges [2016-09-08 11:09:47.961] [log] [info] active reads: 48830 [2016-09-08 11:09:47.963] [log] [info] active reads: 48373 [2016-09-08 11:09:50.042] [log] [info] overlaps 958702 rev_overlaps 469296 [2016-09-08 11:09:50.042] [log] [info] index finished [2016-09-08 11:09:50.043] [log] [info] Number reads 48830 [2016-09-08 11:09:56.855] [log] [info] 0 overlaps [2016-09-08 11:09:56.855] [log] [info] 0 rev overlaps [2016-09-08 11:09:56.924] [log] [info] removed contained reads, active reads: 48373 [2016-09-08 11:09:56.925] [log] [info] active reads: 48373 [2016-09-08 11:09:57.058] [log] [info] 132 killed hinges [2016-09-08 11:09:57.058] [log] [info] 93 hinges [2016-09-08 11:09:57.182] [log] [info] 93 active hinges [2016-09-08 11:09:57.186] [log] [info] Building hinge graph [2016-09-08 11:09:57.195] [log] [info] num hinges 93 [2016-09-08 11:09:57.230] [log] [info] Hinge graph built [2016-09-08 11:09:57.245] [log] [info] after filter 0 active hinges [2016-09-08 11:09:57.271] [log] [info] Starting to build assembly graph. [2016-09-08 11:09:57.443] [log] [info] sort and output finished [2016-09-08 11:09:57.443] [log] [info] version 0.0.3

Thanks in advance for any tips!

alimayy commented 8 years ago

Apologies. Just realised that somehow I emptied my nominal.ini file and the problem was due to that... Closing this.