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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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Tigmint-cut not working correctly #31

Closed majogomezhughes closed 5 years ago

majogomezhughes commented 5 years ago

Hi, I have been trying to run tigmint, but when I run tigmint-cut, the draft.tigmint.fa file comes up empty. I tried it first with a conda-env putting tigmint on it and since it didn't work, I download it directly from the source. Other than that, there is no error on the stderr. 

Started at: 2019-08-05 23:04:06.343181
Reading contig lengths...
Finding breakpoints...

Tool:    bedtools getfasta (aka fastaFromBed)
Version: v2.25.0
Summary: Extract DNA sequences into a fasta file based on feature coordinates.

Usage:   bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> 

Options: 
    -fi Input FASTA file
    -bed    BED/GFF/VCF file of ranges to extract from -fi
    -fo Output file (can be FASTA or TAB-delimited)
    -name   Use the name field for the FASTA header
    -split  given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons)
    -tab    Write output in TAB delimited format.
        - Default is FASTA format.

    -s  Force strandedness. If the feature occupies the antisense,
        strand, the sequence will be reverse complemented.
        - By default, strand information is ignored.

    -fullHeader Use full fasta header.
        - By default, only the word before the first space or tab is used.

Cutting assembly at breakpoints...
DONE!
Ended at: 2019-08-05 23:50:22.002443
lcoombe commented 5 years ago

Hi @majogomezhughes,

The issue is your older version of bedtools, similar to what has been reported in #27 .

Try upgrading your bedtools version to 2.27 (or higher).

Hope that helps! Lauren