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RaverJay / CholerAegon

Pipeline for assembly and antimicrobial resistance gene detection
GNU General Public License v3.0
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prepare fasta error #7

Open JavariaAshraf opened 4 months ago

JavariaAshraf commented 4 months ago

Hi RaverJay, I am trying to use your pipeline from a long time but unable to.Please help me understand and fix this following error.

Error executing process > 'prepare_fasta (24)'

Caused by: Process prepare_fasta (24) terminated with an error exit status (2)

Command executed:

mkdir fixed_name for F in .fa .fasta *.fna; do if [ -e "$F" ]; then ln -s $F fixed_names/VC28_R2.fasta

Command exit status: 2

Command output: (empty)

Command error: .command.sh: line 6: syntax error: unexpected end of file.

I have tried both shortreads and fasta file methods but the error is same. Please guide. Thanks, Javaria

RaverJay commented 4 months ago

Hi, please paste the full command(s) you used and kindly include a preview of the .fasta file you supplied

RaverJay commented 4 months ago

Please retry with the newest version (-r 0.3.1) - fixed some glaring bugs