ilanshom
commented
6 years ago Hi James,
Thanks for pointing that out. There was a small bug in hinge layout. We were actually looking for the parameter del_telomere instead of del_telomeres in the ini file. If you get the latest commit, things should work (Alternatively, you could just change your current ini to del_telomere = 1, but that won't work in future commits)
jwasmuth
Hi, I've set "del_telomeres = 1;" in the .ini but when I run hinge layout it seems to be ignored.
`[2018-03-08 13:02:48.085] [log] [info] Hinging layout [2018-03-08 13:02:48.085] [log] [info] name of db: ecoli, name of .las file ecoli.las [2018-03-08 13:02:48.085] [log] [info] name of fasta: , name of .paf file [2018-03-08 13:02:48.085] [log] [info] filter files prefix: ecoli [2018-03-08 13:02:48.085] [log] [info] output prefix: ecoli [2018-03-08 13:02:48.085] [log] [info] Multiple las files: false [2018-03-08 13:02:48.085] [log] [info] Multiple las files: false [2018-03-08 13:02:48.086] [log] [info] Parameters passed in
[filter] length_threshold = 1000; quality_threshold = 0.23; n_iter = 3; // filter iteration aln_threshold = 1000; min_cov = 5; cut_off = 300; theta = 300; use_qv = true;
[running] n_proc = 36;
[draft] min_cov = 10; trim = 200; edge_safe = 100; tspace = 900; step = 50;
[consensus] min_length = 4000; trim_end = 200; best_n = 1; quality_threshold = 0.23;
[layout] hinge_slack = 1000; min_connected_component_size = 8; del_telomeres = 1; num_events_telomere = 10;
[2018-03-08 13:02:48.207] [log] [info] # Reads: 328553 [2018-03-08 13:02:59.544] [log] [info] Input data finished [2018-03-08 13:02:59.545] [log] [info] LENGTH_THRESHOLD = 1000 [2018-03-08 13:02:59.545] [log] [info] QUALITY_THRESHOLD = 0.23 [2018-03-08 13:02:59.545] [log] [info] ALN_THRESHOLD = 1000 [2018-03-08 13:02:59.545] [log] [info] MIN_COV = 5 [2018-03-08 13:02:59.545] [log] [info] CUT_OFF = 300 [2018-03-08 13:02:59.545] [log] [info] THETA = 300 [2018-03-08 13:02:59.545] [log] [info] N_ITER = 3 [2018-03-08 13:02:59.545] [log] [info] THETA2 = 0 [2018-03-08 13:02:59.545] [log] [info] N_PROC = 36 [2018-03-08 13:02:59.545] [log] [info] HINGE_SLACK = 1000 [2018-03-08 13:02:59.545] [log] [info] HINGE_TOLERANCE = 150 [2018-03-08 13:02:59.545] [log] [info] KILL_HINGE_OVERLAP_ALLOWANCE = 300 [2018-03-08 13:02:59.545] [log] [info] KILL_HINGE_INTERNAL_ALLOWANCE = 40 [2018-03-08 13:02:59.545] [log] [info] MATCHING_HINGE_SLACK = 200 [2018-03-08 13:02:59.545] [log] [info] MIN_CONNECTED_COMPONENT_SIZE = 8 [2018-03-08 13:02:59.545] [log] [info] USE_TWO_MATCHES = true [2018-03-08 13:02:59.545] [log] [info] del_telomeres = false [2018-03-08 13:02:59.922] [log] [info] read mask finished [2018-03-08 13:03:00.021] [log] [info] read marked repeats [2018-03-08 13:03:00.021] [log] [info] killed 0 reads with many repeats `
I've tried setting it to true and TRUE but hinge still reports "false". Is this intended behaviour?
Thanks James