search

wwood / finishm

genome improvement and finishing without further sequencing effort
MIT License
5 stars 2 forks source link

finishm assemble problem #6

Closed wwood closed 9 years ago

wwood commented 9 years ago

This should assemble better

ben@ben:~$ ~/git/priner/bin/finishm assemble --already-assembled-velvet-directory /srv/home/s4293811/testing_files/testing_graftM/comparison_hmmalign_pynast_nhmmer/forward/pynast/mock1_rep1_nextera/felvet/F_f__Enterobacteriaceae_4306_assembly.fa/ --output-contigs /dev/stdout --post-assembly-coverage-cutoff 60 --output-pathspec --assemble-from 1593s --bubbly --recoherence-kmer 77 |describeFasta.pl 
 INFO finishm 08/12 14:42:18: Using previous assembly stored in /srv/home/s4293811/testing_files/testing_graftM/comparison_hmmalign_pynast_nhmmer/forward/pynast/mock1_rep1_nextera/felvet/F_f__Enterobacteriaceae_4306_assembly.fa/
 INFO finishm 08/12 14:42:18: Reading in the actual sequences of all reads from /srv/home/s4293811/testing_files/testing_graftM/comparison_hmmalign_pynast_nhmmer/forward/pynast/mock1_rep1_nextera/felvet/F_f__Enterobacteriaceae_4306_assembly.fa/CnyUnifiedSeq
 INFO finishm 08/12 14:42:18: Read in 4306 sequences
 INFO finishm 08/12 14:42:18: Parsing the graph output from velvet
 INFO finishm 08/12 14:42:18: Finished parsing graph: found 5809 nodes and 7691 arcs
 INFO finishm 08/12 14:42:18: Beginning parse of graph using velvet's parsing C code..
 INFO finishm 08/12 14:42:19: Completed velvet code parsing velvet graph
 INFO finishm 08/12 14:42:19: Removing nodes with coverage < 60.0 from graph..
 INFO finishm 08/12 14:42:19: Removed 4600 nodes and 6483 arcs, leaving 1209 nodes and 1208 arcs.
 INFO finishm 08/12 14:42:19: Starting to assemble from 1593s..
 INFO finishm 08/12 14:42:19: Assembling from: 1593s
Number  Name    Length
1   1593s   724

Also, running finishm assemble without specifying a start node and using the progress bar has issues, it is over-incremented and so errors out.

wwood commented 9 years ago

it does now, at least in the variants branch which will soon be merged