Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
Hi
I was trying to run Haploclique on a subset of HCV RNA data referred in your paper (Illumina MiSeq NGS , 1000X coverage, 6926 paired end reads, reference ~ 9720 bp). The script execution seems to stall with only this message -
mv: cannot move x*-dir' to a subdirectory of itself,x*-dir/alignment.prior'
Here is a snippet of the debug log for the script haploclique-assembly
mv 'x-dir' 'x-dir/alignment.prior'
mv: cannot move x*-dir' to a subdirectory of itself,x_-dir/alignment.prior'
parallel computeParallelSingle '{}' ::: 'x_-dir'
The code seems to take a huge time to execute haploclique under computeParallelSingle(). Am I missing some parameter setting ? Your help in debugging this is much appreciated.
Additionally, could you provide a pointer to the simulated HIV data from the paper ?
Thanks very much !
Hi I was trying to run Haploclique on a subset of HCV RNA data referred in your paper (Illumina MiSeq NGS , 1000X coverage, 6926 paired end reads, reference ~ 9720 bp). The script execution seems to stall with only this message - mv: cannot move
x*-dir' to a subdirectory of itself,x*-dir/alignment.prior'Here is a snippet of the debug log for the script haploclique-assembly
$ bash -x haploclique-assembly -r HCV1.fasta -i HCV1_reads_sorted.bam ... ...
x*-dir' to a subdirectory of itself,x_-dir/alignment.prior'The code seems to take a huge time to execute haploclique under computeParallelSingle(). Am I missing some parameter setting ? Your help in debugging this is much appreciated. Additionally, could you provide a pointer to the simulated HIV data from the paper ? Thanks very much !