search

alekseyzimin / masurca

GNU General Public License v3.0
243 stars 35 forks source link

Ploidy estimation wrong ! #73

Open jnarayan81 opened 5 years ago

jnarayan81 commented 5 years ago

Estimate ploidy wrongly ! I expected it to be 2 ...

➜  MASURCA_all ./assemble.sh
[Fr Okt 19 15:27:18 CEST 2018] Processing pe library reads
[Fr Okt 19 15:38:33 CEST 2018] Average PE read length 250
[Fr Okt 19 15:38:34 CEST 2018] Using kmer size of 83 for the graph
[Fr Okt 19 15:38:34 CEST 2018] MIN_Q_CHAR: 33
[Fr Okt 19 15:38:34 CEST 2018] Creating mer database for Quorum
[Fr Okt 19 15:46:07 CEST 2018] Error correct PE.
[Fr Okt 19 16:34:44 CEST 2018] Estimating genome size.
[Fr Okt 19 16:40:48 CEST 2018] Estimated genome size: 191455832
[Fr Okt 19 16:40:48 CEST 2018] Creating k-unitigs with k=83
[Fr Okt 19 17:11:04 CEST 2018] Computing super reads from PE 
Using CABOG from is /home/urbe/Tools/masurca/MaSuRCA-3.2.8/bin/../CA8/Linux-amd64/bin
Running mega-reads correction/assembly
Using mer size 15 for mapping, B=17, d=0.029
Estimated Genome Size 191455832
Estimated Ploidy 1
Using 40 threads
Output prefix mr.41.15.17.0.029
Pacbio coverage >30x, using 30x of the longest reads
Reducing super-read k-mer size
Mega-reads pass 1
Running locally in 1 batch
TimothyStephens commented 5 years ago

Hi,

I am also having the same problem. Would it be worth re-running the assembly with a ploidy of 2 set manually?

Thanks, Tim.

tinavisnovska commented 5 years ago

Experiencing the same issue as well, should I get ploidy 2 for diploid species and 1 for haploid? Does the estimate affect the outcome?

Cheers.

sunnvor commented 5 years ago

I also get Estimated ploidy 1 when assembling a diploid species. Has anyone figured out if this affects the assembly?

asan-emirsaleh commented 3 years ago

All you have the same error (e.g. 'Error correct PE')?