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raunaqm / MLEHaplo

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Issue running construct_graph.pl #3

Open dr-artio opened 8 years ago

dr-artio commented 8 years ago

I tied to run all steps using data SRR961514.sra On the step 3 when I run script it was running for a while and finished but output file was not produced. How long should this step take? Why it did not generate output file?

raunaq-m commented 8 years ago

Hi @night-stalker

Sorry for the delay in response. I have been unfortunately locked out of this account. The new repository is maintained at https://github.com/raunaq-m/MLEHaplo. Let me try it on the data and get back to you.

raunaq-m commented 8 years ago

Hi @night-stalker I ran the script "construct_graph.pl" using the following inputs and got an output file:

time perl construct_graph.pl SRR961514.combined.fasta SRR961514.all.MR.59 3 test_graph "s"

It took about 2 hours to finish. SRR961514.combined.fasta : is the combined fasta file (read1 and read2 paired end files) SRR961514.all.MR.59 : is the error corrected set of k-mers generated by MultiRes 3 : k-mer counts threshold test_graph: Output graph file (Which contains around 667K lines) "s"