The file cannot be accessed by the system.

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Anna Gregory

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May 3, 2021, 11:38:37 PM5/3/21
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Hi All, 

I used "sudo apt install" to install AByss and then ran a de novo assembly with 2x150 bp sequencing. The sequence seems to have gone okay since I didn't receive any error messages. However, when I try to access the word and/or FASTA the files, I'm told that "Word is unable to read this file" or "The file cannot be accessed by the system" (when I try to open the FASTA contigs file in notepad). I am able to access the stats excel sheet. My ultimate goal is to analyze the assembly in quast and to do that I need the FASTA file. 

Does anyone have any thoughts on where I can troubleshoot in installing or running the assembly to gain access to the outputs? 

Lauren Coombe

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May 3, 2021, 11:41:13 PM5/3/21
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Hi Anna,

Have you tried opening the fasta files from the command line using 'less' or 'more', for example? I'd suggest trying this way vs. using applications like word, which are not really always designed to read fasta files. You will likely run QUAST from the command line as well, so it's most important that you can access the file OK using unix commands. You could also try running 'abyss-fac' on the fasta file(s) to assess the contiguity reference-free.

Hope that helps,
Lauren

Anna Gregory

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May 4, 2021, 12:16:44 PM5/4/21
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Hi Lauren, 

You made such a good point! I was able to access the file through a QUAST from the command line. Thank you!

Lauren Coombe

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May 4, 2021, 12:17:21 PM5/4/21
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Hi Anna,

Excellent! Glad everything's working for you :)

Thank you for your interest in ABySS!
Lauren

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