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cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
GNU General Public License v3.0
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Empty output files #47

Closed ruby-r closed 6 years ago

ruby-r commented 7 years ago

Hello. when I run haploclique-assembly, i get the output files (the latter 7 of which are 0 bytes):

consensus.fasta statistics.txt deletions.txt alignment.prior data_clique_to_reads.tsv data_cliques_paired_R1.fastq data_cliques_paired_R2.fastq data_cliques_single.fastq quasispecies.fasta singles.prior

and the following error:

[E::hts_open_format] fail to open file 'single_sort.bam' samtools view: failed to open "single_sort.bam" for reading: No such file or directory rm: single_sort.bam: No such file or directory mv: rename x-dir to x-dir/alignment.prior: Invalid argument cat: alignment.prior: No such file or directory STATUS Cliques/Uniques/CPU time: 0/0/0 Error correction of singletons cat: x/data_cliques_paired_R1.fastq: No such file or directory cat: x/data_cliques_paired_R2.fastq: No such file or directory cat: x/data_cliques_single.fastq: No such file or directory cat: x/data_clique_to_reads.tsv: No such file or directory Max read length: 0 bp mv: rename x-dir to x-dir/alignment.prior: Invalid argument cat: alignment.prior: No such file or directory STATUS Cliques/Uniques/CPU time: 0/0/0 cat: x/data_cliques_paired_R1.fastq: No such file or directory cat: x/data_cliques_paired_R2.fastq: No such file or directory cat: x/data_cliques_single.fastq: No such file or directory cat: x/data_clique_to_reads.tsv: No such file or directory Max read length: 0 bp

I have all of the dependencies installed (and updated). I would greatly appreciate any advice as to what this error message means and how to rectify it. thank you!

MaryamZaheri commented 7 years ago

Hi, Why don't you use the current version of Haploclique (the current master branch)?