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wwood / finishm

genome improvement and finishing without further sequencing effort
MIT License
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Error running gapfill #16

Open ctSkennerton opened 9 years ago

ctSkennerton commented 9 years ago 
INFO bio-velvet 20/01 12:17:53: Running velveth: /home/cts/local/finishm/lib/assembly/../../ext/src/velveth /tmp/d20150120-12888-zb9hue 51  -fasta -short /tmp/probes.fa20150120-12888-daaygv -fastq -shortPaired C00003105.reads.fastq -create_binary
INFO bio-velvet 20/01 12:21:25: Running velvetg: /home/cts/local/finishm/lib/assembly/../../ext/src/velvetg /tmp/d20150120-12888-zb9hue -read_trkg yes -cov_cutoff 3.5 -tour_bus no -read_to_node_binary yes
 INFO finishm 20/01 12:33:21: Finished running assembly
 INFO finishm 20/01 12:33:21: Reading in the actual sequences of all reads from /tmp/d20150120-12888-zb9hue/CnyUnifiedSeq
 INFO finishm 20/01 12:33:23: Read in 7489828 sequences
ERROR finishm 20/01 12:33:23: Probe sequence #1543 has changed - perhaps the wrong velvet assembly directory was specified, or a fresh assembly is required?
/home/cts/local/finishm/lib/assembly/graph_generator.rb:130:in `generate_graph': Probe sequences changed since previous velvet assembly! (RuntimeError)
    from /home/cts/local/finishm/lib/finishm/gapfiller.rb:153:in `run'
    from /home/cts/local/finishm/bin/finishm:124:in `<main>'
wwood commented 9 years ago

Hey,

OK, I think I have some data at ACE that gives the same problem, or just need to make the tests work. roundup mode is better beta tested, if that is helpful - you can run it with --gapfill-only as well.