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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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Error: Unable to access jarfile /ConsensusFixer.jar #53

Closed zusman closed 6 years ago

zusman commented 6 years ago

The haploclique-assembly can not find ConsensusFixer jar file and there is no detail on where to put this jar file. Can you please let me know how to resolve it? I have already tried placing the said .jar file in bin build and external folders.

$ haploclique-assembly -r hbv_refseq.fasta -i C7_mapped.bam Error: Unable to access jarfile /ConsensusFixer.jar [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: cannot remove ‘single_sort.bam’: No such file or directory STATUS: 169 Cliques/Uniques/CPU time: 62/41/1 STATUS: 200 Cliques/Uniques/CPU time: 100/52/1 Error correction of singletons Max read length: 378 bp STATUS: 47 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: 378 bp [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] mv: cannot stat ‘single_2.bam’: No such file or directory

armintoepfer commented 6 years ago

The latest master version does not even use ConsensusFixer. Please use the latest HEAD