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tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
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snippy multi prompting unreadable file #428

Open furqan915 opened 4 years ago

furqan915 commented 4 years ago

Hi,

I have tried generating tab file by pasting all the filenames and paths in excel and later converted that CSV file using this command.

sed -e 's/,/\t/g' input.csv > input2.tab

and then ran the following command and this message showed up:

root@honey-pc:/home/fan/monas/fna# snippy-multi input2.tab --ref /home/fan/monas/fna/GCF_genomic.fna --cpus 4 > runme.sh Reading: input2.tab ERROR: [GCF_genomic.fna ] unreadable file '/home/fan/monas/fna/GCF_genomic.fna

Could you please guide me on how to create input.tab file in Linux command line (without using excel and csv format if there is a problem with formatting the file)?

Secondly, I have already checked .fna format is acceptable and properly working with snippy. But this unreadable shows up in snippy-multi.

Regards

furqan915 commented 4 years ago

Hi,

Thanks everyone! for previously raising issues and guided me well. The following are the commands that helped me in building input.tab file for running snippy-multi. These commands could be helpful for persons with limited knowledge of Linux.

To save filenames as ID ls > file1.txt To save filenames with their paths as contigs find $(pwd)/*.fna > file2.txt To combine both files columnwise and have tabs paste file1.txt file2.txt > file3.txt

Then run the snippy multi commands as mentioned in the readme. Thanks to Torsten Seeman and other developers.

schultzm commented 4 years ago

@tseemann I think this issue can be closed now.