qichao1984
commented
4 years ago Hi, two quick questions: Have you installed diamond in your linux system? Have you modified the perl script to include the correct path of diamond? If not, can you try that?
From: ChristianFurbo notifications@github.com Sent: Tuesday, October 29, 2019 9:12:11 PM To: qichao1984/NCyc NCyc@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [qichao1984/NCyc] Cannot find diamond output (#10)
Hi. :) I am trying to run the following:
perl NCycProfiler.PL -d ~/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces -m diamond -f fasta -s prot -si /home/christian/Bioinformatic_programs/NCyc-master/FileForNcyc.txt -o PC_Ncyc
However, I get the following error:
cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10786.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10787.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10788.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10789.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10790.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10791.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10792.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10793.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10794.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10795.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10796.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10797.diamond': No such file or directory was not found in /home/christian/Bioinformatic_programs/NCyc-master/FileForNcyc.txt, please check!
My tab delimited file looks like this: head FileForNcyc.txt AAsequencesF10786 18190 AAsequencesF10787 10828 AAsequencesF10788 41144 AAsequencesF10789 44519 AAsequencesF10790 874 AAsequencesF10791 81255 AAsequencesF10792 61666 AAsequencesF10793 79880 AAsequencesF10794 63433 AAsequencesF10795 51039
Maybe, the problem is trivial, however I cant see how to fix it? :) Also, I tried with usearch, got the same problem
Cheers
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ChristianFurbo
Hi. :) I am trying to run the following:
perl NCycProfiler.PL -d ~/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces -m diamond -f fasta -s prot -si /home/christian/Bioinformatic_programs/NCyc-master/FileForNcyc.txt -o PC_Ncyc
However, I get the following error:
cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10786.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10787.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10788.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10789.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10790.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10791.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10792.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10793.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10794.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10795.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10796.diamond': No such file or directory cp: cannot stat '/home/christian/Desktop/scripts_to_abacus/From_abacus/PC_AA_Seqeunces/AAsequencesF10797.diamond': No such file or directory was not found in /home/christian/Bioinformatic_programs/NCyc-master/FileForNcyc.txt, please check!
My tab delimited file looks like this: head FileForNcyc.txt AAsequencesF10786 18190 AAsequencesF10787 10828 AAsequencesF10788 41144 AAsequencesF10789 44519 AAsequencesF10790 874 AAsequencesF10791 81255 AAsequencesF10792 61666 AAsequencesF10793 79880 AAsequencesF10794 63433 AAsequencesF10795 51039
Maybe, the problem is trivial, however I cant see how to fix it? :) Also, I tried with usearch, got the same problem
Cheers