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churchlab / millstone

Genome engineering and analysis software
http://churchlab.github.io/millstone/
MIT License
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Millstone not collecting unused reads for contig assembly use #668

Open mnapolitano89 opened 8 years ago

glebkuznetsov commented 8 years ago

Can you describe how you figured this out?

mnapolitano89 commented 8 years ago

The error in the celery logs indicated that it was trying to assemble 0 reads :(

glebkuznetsov commented 8 years ago

Cool, wouldn't hurt if you could paste that error and anything relevant looking above or below.

On Thu, May 26, 2016 at 4:28 PM mnapolitano89 notifications@github.com wrote:

The error in the celery logs indicated that it was trying to assemble 0 reads :(

— You are receiving this because you commented.

Reply to this email directly or view it on GitHub https://github.com/churchlab/millstone/issues/668#issuecomment-221985076

mnapolitano89 commented 8 years ago

my inability to know how to use vim makes me do this: [0.000042] Reading read set file /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1/Sequences; [0.000049] 0 sequences found [0.000050] 0 sequences in total. [0.000061] Writing into roadmap file /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1/Roadmaps...

[2016-05-26 16:32:50,647: WARNING/Worker-4] velvetg cmd: [2016-05-26 16:32:50,647: WARNING/Worker-4] /home/ubuntu/millstone/genome_designer/conf/../tools/velvet/velvetg /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1 -ins_length 284 -exp_cov 22.7934022229 -ins_length_sd 233 -cov_cutoff 5.69835055573 -min_contig_lgth 200 -read_trkg yes [0.000000] Reading roadmap file /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1/Roadmaps

[0.000171] Initial node count 0 [0.000171] Removed 0 null nodes [0.000171] Concatenation over! [0.000172] Removing reference contigs with coverage < 5.698351... [0.000172] Concatenation... [0.000173] Renumbering nodes [0.000173] Initial node count 0 [0.000173] Removed 0 null nodes [0.000174] Concatenation over! [0.000184] Writing contigs into /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1/contigs.fa... [0.000194] Writing into stats file /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1/stats.txt... [0.000212] Writing into graph file /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/6690444a/alignment_groups/1f263265/sample_alignments/212c2eef/assembly/1/LastGraph... [0.000237] EMPTY GRAPH

Final graph has 0 nodes and n50 of 0, max 0, total 0, using 0/0 reads [2016-05-26 16:32:50,668: ERROR/MainProcess] Task genome_finish.assembly.generate_contigs[dc5d7eb8-d7e4-431b-b817-f75c6029548b] raised unexpected: IndexError('list index out of range',) Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/celery/app/trace.py", line 240, in trace_task R = retval = fun(_args, _kwargs) File "/usr/local/lib/python2.7/dist-packages/celery/app/trace.py", line 438, in protected_call return self.run(_args, _kwargs) File "/home/ubuntu/millstone/genome_designer/genome_finish/celery_task_decorator.py", line 57, in wrapper raise exc IndexError: list index out of range [2016-05-26 16:32:52,890: INFO/MainProc