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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
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miniasm_and_minipolish.sh #60

Closed sogriffin98 closed 1 year ago

sogriffin98 commented 1 year ago

Hello,

I am trying to follow the 'Assemblies' instructions on the Generating Assemblies Wiki (https://github.com/rrwick/Trycycler/wiki/Generating-assemblies).

I have ran this code: python3 miniasm_and_minipolish.sh /data/ssd2/sgriffin/fallax/Genome_Assembly/Trycycler/read_subsets/sample_02.fastq "$threads" > /data/ssd2/sgriffin/fallax/Genome_Assembly/Trycycler/assemblies/assembly_02.gfa && any2fasta /data/ssd2/sgriffin/fallax/Genome_Assembly/Trycycler/assemblies/assembly_02.gfa > /data/ssd2/sgriffin/fallax/Genome_Assembly/Trycycler/assemblies/assembly_02.fasta

and I get the following error message: File "/home/sgriffin/Minipolish/miniasm_and_minipolish.sh", line 12 overlaps=$(mktemp)".paf" ^ SyntaxError: invalid syntax

I was wondering if the issue is just me or is it a more general issue?

Thank you :)

rrwick commented 1 year ago

I think the problem is that you're running miniasm_and_minipolish.sh through Python, but it's a Bash script not a Python script.

Change python3 miniasm_and_minipolish.sh to ./miniasm_and_minipolish.sh, and it should work! Or if you copy miniasm_and_minipolish.sh to somewhere in your PATH variable (e.g. /usr/local/bin or ~/.local/bin), then you can just run miniasm_and_minipolish.sh (without the leading ./).

Ryan