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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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The tool returned zero bytes of wtasm.dmo.cns.log, wtasm.dmo.cns, and wtasm.dmo.lay.utg #56

Open ChooseelBunsuwansakul opened 2 years ago

ChooseelBunsuwansakul commented 2 years ago 
(base) chooseel@chooseels-MacBook-Pro smartdenovo % ./smartdenovo.pl -c 1 /Users/chooseel/Desktop/20220401-08_phage_nanopore_sequencing/seqtk/phage_OxfordNanopore.fa > phage.mak
(base) chooseel@chooseels-MacBook-Pro smartdenovo % make -f phage.mak
./wtpre -J 5000 /Users/chooseel/Desktop/20220401-08_phage_nanopore_sequencing/seqtk/phage_OxfordNanopore.fa | gzip -c -1 > wtasm.fa.gz
./wtzmo -t 8 -i wtasm.fa.gz -fo wtasm.dmo.ovl -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000
[Fri Jun 24 11:06:38 2022] loading long reads
[Fri Jun 24 11:06:38 2022] Done, 15494 reads (length >= 0)
[Fri Jun 24 11:06:38 2022] sorted sequences by length dsc
[Fri Jun 24 11:06:38 2022] calculating overlaps, 8 threads
[Fri Jun 24 11:06:38 2022] indexing 1/1
[Fri Jun 24 11:06:38 2022] - scanning kmers (16 bp)
15494 reads
[Fri Jun 24 11:06:45 2022] - high frequency kmer depth is set to 100
[Fri Jun 24 11:06:45 2022] - average kmer depth = 13
[Fri Jun 24 11:06:45 2022] - 20588 high frequency kmers (>=100)
[Fri Jun 24 11:06:45 2022] - indexing 1056137 kmers
15494 reads
[Fri Jun 24 11:06:53 2022] Done
[Fri Jun 24 11:06:53 2022] querying 1/1
progress: 15494 13112 100.00%, 284.04 CPU seconds
[Fri Jun 24 11:07:15 2022] Done
./wtclp -i wtasm.dmo.ovl -fo wtasm.dmo.obt -d 3 -k 300 -m 0.1 -FT
[Fri Jun 24 11:07:15 2022] loading alignments
[Fri Jun 24 11:07:15 2022] 12741
[Fri Jun 24 11:07:15 2022] Done, 5081 reads, 12741 overlaps
[Fri Jun 24 11:07:15 2022] clipping based on overlap depth
Before: legal overlaps = 4348
After:  legal overlaps = 2106
[Fri Jun 24 11:07:15 2022] Done
0 reads were filtered by connection-checking
9 reads were truncated by chimera-checking
legal overlaps = 2139
[Fri Jun 24 11:07:15 2022] Done
--------------------------------
== Message for debug ==
Sequence coverage statistic:
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0
           0           0           0           0           0           0           0           0           0           0

Total aviable sequences: 14029185 bp
Average Coverage(?):     2
Genome Size(?):          7014592 bp
--------------------------------
[Fri Jun 24 11:07:15 2022] output
[Fri Jun 24 11:07:15 2022] Done
./wtlay -i wtasm.fa.gz -b wtasm.dmo.obt -j wtasm.dmo.ovl -fo wtasm.dmo.lay -w 300 -s 200 -m 0.1 -r 0.95 -c 1
[Fri Jun 24 11:07:15 2022] loading reads
[Fri Jun 24 11:07:16 2022] Done, 15494 reads
[Fri Jun 24 11:07:16 2022] loading reads obt information
[Fri Jun 24 11:07:16 2022] Done
[Fri Jun 24 11:07:16 2022] loading alignments
loaded 2071 overlaps
building edges
1976 fine overlaps
[Fri Jun 24 11:07:16 2022] Done
[Fri Jun 24 11:07:16 2022] calculating edge coverage ...
[Fri Jun 24 11:07:16 2022] removed 99 duplicate edges
[Fri Jun 24 11:07:16 2022] Done
[Fri Jun 24 11:07:16 2022] masked 399 contained reads
[Fri Jun 24 11:07:16 2022] masked 30 low coverage (<1) edges
[Fri Jun 24 11:07:16 2022] 'best_overlap' cut 452 non-best edges
8 tips, 0 bubbles, 0 chimera, 0 non-bog, 0 recoveries
[Fri Jun 24 11:07:16 2022] repair 8 bog elements
0 tips, 0 bubbles, 0 chimera, 0 non-bog, 0 recoveries
[Fri Jun 24 11:07:16 2022] generated 10842 unitigs
[Fri Jun 24 11:07:16 2022] recovered 0 edges inter unitigs
0 tips, 0 bubbles, 0 chimera, 0 non-bog, 0 recoveries
[Fri Jun 24 11:07:16 2022] generated 10842 unitigs
[Fri Jun 24 11:07:16 2022] recover 0 edges inter unitigs
[Fri Jun 24 11:07:16 2022] output 0 independent unitigs
[Fri Jun 24 11:07:16 2022] Done
./wtcns -t 8 wtasm.dmo.lay > wtasm.dmo.cns 2> wtasm.dmo.cns.log
(base) chooseel@chooseels-MacBook-Pro smartdenovo %

How to fix this.

Thank you in advance.

ruanjue commented 2 years ago

Maybe the contigs are too short, please set the option u to a small value (1 or 2) in wtlay.

 -u <int>    Min nodes of a layout to be output as independent unitig, [4]