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no consensus fasta file produced #15
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Hi there. When you need code developers to debug a problem (for shiver but also in general), you need to provide enough detail for them to figure out the problem. To start with, what were the exact commands you ran and what was all of the output printed to the command line as a result of those commands? |
Here are the command and the output messages: A different dataset produced good result with the same command. It produced _shiverBuild_cut_wRefs.fasta file. |
As explained in the manual, shiver_align_contigs only produces a _cut_wRefs.fasta file if contig correction is needed; the last line of the output above states that contig correction was not needed. |
I have been trying to use shiver for a set of illumina data. SPAdes produced a single good and long HIV contig. shiver_align_contigs.sh produced a _shiverBiuld_raw_wRefs.fasta , but not a _shiverBiuld_cut_wRefs.fasta. shiver_map_reads.sh did not produce a consensus fasta file. What could be the problem? Thanks.
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