DBdust with HINGE

[mictadlo]

Hi, I tried to use DBdust but I got in daligner step daligner: Track 'dust' annotation file is junk with the following commands (https://github.com/thegenemyers/DALIGNER/issues/73).

By any chance do you know what I did wrong?

Thank you in advance.

Michal

[govinda-kamath]

I've not used DBdust in a long time. We had tried it when we first started, but it seemed to raise some complaints like this and did not really help much. Hence we skipped the step.

[mictadlo]

By any chance, do you know any alternatives to DBdust?

[mictadlo]

Hi, I got Segmentation fault

mkdir: cannot create directory ‘log’: File exists
[2018-02-01 12:18:51.359] [log] [info] Reads filtering
[2018-02-01 12:18:51.360] [log] [info] name of db: plantDB, name of .las file plant
[2018-02-01 12:18:51.360] [log] [info] name of fasta: , name of .paf file 
[2018-02-01 12:18:51.374] [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 = 8;

[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; 
aggressive_pruning = 1;

[2018-02-01 12:18:52.402] [log] [info] Las files: plant
[2018-02-01 12:18:52.402] [log] [info] Calling glob.
plant.1.las
-------------------------
Number of files 0
Input string plant
-------------------------
[2018-02-01 12:18:52.402] [log] [info] # Reads: 8234303
(null): .qual-track does not exist for this db.
[2018-02-01 12:25:26.218] [log] [info] No debug restrictions.
/scratch/waterhouse_team/HINGE-without-dust/HINGE/inst/bin/hinge: line 8: 135246 Segmentation fault      (core dumped) Reads_filter "$@"
[2018-02-01 12:57:57.521] [log] [info] Getting maximal reads
[2018-02-01 12:57:57.521] [log] [info] name of db: plantDB, name of .las file plant
[2018-02-01 12:57:57.521] [log] [info] name of fasta: , name of .paf file 
[2018-02-01 12:57:57.533] [log] [info] Parameters passed in

ls
-rw-rw---- 1 lorencm default 3.0G Jan 31 09:58 plantDB.9.las
-rw-rw---- 1 lorencm default 195K Jan 31 11:04 .plantDB.9.qual.anno
-rw-rw---- 1 lorencm default 2.1M Jan 31 11:04 .plantDB.9.qual.data

Commands which I used:

cd /scratch/waterhouse_team/HINGE-without-dust/HINGE

module load cmake/3.6.1-foss-2017a hdf5/1.8.18-foss-2017a-nompi boost/1.64.0-foss-2017a-python-2.7.13
source utils/setup.sh
#mkdir -p data/plant
cd data/plant
mkdir log

hinge filter --db plantDB --las plant --mlas -x plant --config ../../utils/nominal.ini
hinge maximal --db plantDB --las plant --mlas -x plant --config ../../utils/nominal.ini
hinge layout --db plantDB --las plant.las -x plant --config ../../utils/nominal.ini -o plant
hinge clip plant.edges.hinges plant.hinge.list demo
hinge draft-path $PWD plant plantdemo.G2.graphml
hinge draft --db plantDB --las plant.las --prefix plant --config ../../utils/nominal.ini --out plant.draft

hinge correct-head plant.draft.fasta plant.draft.pb.fasta draft_map.txt
fasta2DB draft plant.draft.pb.fasta

What did I miss?

Thank you in advance.

Michal