CAP3 for DNA assembly

I'm using CAP3 for 1st time, I have checked tutorial and gave input file "genome.fasta" as shown below. I have used the below command to run:

cap3 genome.fasta > output.txt

I got error: Cannot open genome.fasta.

Can anyone pls help to solve this?

>scaffold00017
ATATAAAGCATAAATCGATTAGAAATGAAACCTTCTCAAATCATGAATAagaataatattcttcTAAATGAAGATAAGATTGATCCTAAAGATCTTATGATATTAAAATTAGTAAAAGAATCAGGATAATCTGAATACCGCCGAGGTATTCCATTTAACCCTAAAAAATGTTGAGGAAAAAAAGTCAAATTAACACCTAAAAACATCACTAAAAATTGAGTTTTAAGCACTATTTCATTAAAAGAGATACCAAAAAGTGTTGGAAATCAAAAAGTTACTGCTCCAAAAATAGCAAAAACTGCTCCTATAGATAATACATAATGAAAATGAGCTACTACGTAATAAGTATCATGAAGAATAATATCAATTGAAGAATTAGATAATATAATACCAGTTAATCCCCCCAACGTGAATAAAAataaaaatCCTAAACATCATAATATAGGAGAAT
>scaffold0001
AATATAATTATATATTTACCTGCTCCTTCAAATATCAATTATTTTTGAAACTTAGGGTCTCTTATTGGGATCATATTAATAATTCAAATCGTTTCTGGTTtttttttATCTCTTCATTACTTGTCTTCTATAGAAGAAGCTTTTTATTCAGTTAATCATATCAGCCGAGAAGTATATATAGGGTGATTAGTTCGATTTTTTCATATCAATGGAGCATCGGCTTTTttctttttgattttttctcatattttaaaAAACATTATAAACTCATCATGAAAGTTTACTAATCTGTGAATATCAGGGGTAACCATTCTATTGATTTCTATAGCAACAGCTTTTGTAGGATATGTTTTACCATGAGGCCAAATATCTTTTTGAGCAGCTACTGTAATTACTAATTTAT
>scaffold00011
CCAATATACCAGTAAAAACaaatataatcaa

cap3

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updated 3.9 years ago by GenoMax

• written 3.9 years ago by dhananya •

Hello dhananya,

Welcome to the forum.

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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written 3.9 years ago by lieven.sterck

output of ls -lah genome.fa ?

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written 3.9 years ago by Pierre Lindenbaum

yes.

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written 3.9 years ago by dhananya •

Show actual output. yes is not expected output of the command @Pierre asked for.

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written 3.9 years ago by GenoMax

How is that fasta file you show there called? if it's not genome.fasta you will need to give it the name the file has in your case.

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written 3.9 years ago by lieven.sterck

Thank you. Yes I gave name as genome.fasta

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written 3.9 years ago by dhananya •

0 answers

No answers yet.

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