Two files found as same file and not in si

[edisagarcia]

Hi! Thanks for creating this useful tool. I have an error that I cant solve, even using the new script uploaded 20 days ago.

My command is perl NCycProfiler2.PL -d . -m diamond -f .faa -s prot -si sampleinfi.txt -o output14

and apparenty eveything tus fine but this is the last lines of the file:

Total time = 917.505s Reported 698857 pairwise alignments, 698891 HSPs. 698857 queries aligned. cp: './proteins_aa14diamond' and './proteins_aa14diamond' are the same file was not found in sampleinfi.txt, please check!

this is my -si sampleinfi.txt

and the files I have in the folder with the script file are: data NCycProfiler2.PL proteins_aa14.faa diamond NCycProfiler.PL README.md diamond_manual.pdf LICENSE proteins_aa14diamond sampleinfi.txt

Can you please, please help me?

Thanks in advance,

Ed

[qichao1984]

perhaps something wrong with the -f option, please try the following: perl NCycProfiler2.PL -d . -m diamond -f faa -s prot -si sampleinfi.txt -o output14

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From: edisagarcia notifications@github.com Sent: Tuesday, January 19, 2021 7:07:27 PM To: qichao1984/NCyc NCyc@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [qichao1984/NCyc] Two files found as same file and not in si (#17)

Hi! Thanks for creating this useful tool. I have an error that I cant solve, even using the new script uploaded 20 days ago.

My command is perl NCycProfiler2.PL -d . -m diamond -f .faa -s prot -si sampleinfi.txt -o output14

and apparenty eveything tus fine but this is the last lines of the file:

Total time = 917.505s Reported 698857 pairwise alignments, 698891 HSPs. 698857 queries aligned. cp: './proteins_aa14diamond' and './proteins_aa14diamond' are the same file was not found in sampleinfi.txt, please check!

this is my -si sampleinfi.txthttps://github.com/qichao1984/NCyc/files/5835454/sampleinfi.txt

and the files I have in the folder with the script file are: data NCycProfiler2.PL proteins_aa14.faa diamond NCycProfiler.PL README.md diamond_manual.pdf LICENSE proteins_aa14diamond sampleinfi.txt

Can you please, please help me?

Thanks in advance,

Ed

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[edisagarcia]

Thanks a lot for your reply!

Uhm no, it still the same problem. cp: './proteins_aa14diamond' and './proteins_aa14diamond' are the same file was not found in sampleinfi.txt, please check!

Any other idea what it might be? Thanks in advance, Ed

[qichao1984]

Have you deleted previous files? I do not expect "proteins_aa14diamond" as output, but "proteins_aa14.diamond". In addition, you may also rename your file as proteins_aa14.fasta. This might be the reason.

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From: edisagarcia notifications@github.com Sent: Tuesday, January 19, 2021, 20:42 To: qichao1984/NCyc Cc: Qichao Tu; Comment Subject: Re: [qichao1984/NCyc] Two files found as same file and not in si (#17)

Thanks a lot for your reply!

Uhm no, it still the same problem. cp: './proteins_aa14diamond' and './proteins_aa14diamond' are the same file was not found in sampleinfi.txt, please check!

Any other idea what it might be? Thanks in advance, Ed

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/qichao1984/NCyc/issues/17#issuecomment-762817029, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNORGHIZBX7JACDGMIRK6TS2V44BANCNFSM4WITOWTQ.

[edisagarcia]

HI, I deleted other files that and rename the files to proteins14.fasta. Actually, now in the error appears as proteins14.diamond. However, the problem still the same.

cp: ‘./proteins14.diamond’ and ‘./proteins14.diamond’ are the same file was not found in sampleinfi.txt, please check!

Is there a way to solve this? Thanks so much for your help.

[edisagarcia]

My protein fasta sequences are ORFs predicted with prodigal. Maybe there is an issue with diamond?

[qichao1984]

This should be still an issue related not finding “good” diamond files in the path. The “diamond” program in your path may be the cause, try move it somewhere else.

发件人: edisagarciamailto:notifications@github.com 发送时间: Wednesday, January 20, 2021 7:06 AM 收件人: qichao1984/NCycmailto:NCyc@noreply.github.com 抄送: Qichao Tumailto:philloid@gmail.com; Commentmailto:comment@noreply.github.com 主题: Re: [qichao1984/NCyc] Two files found as same file and not in si (#17)

My protein fasta sequences are ORFs predicted with prodigal. Maybe there is an issue with diamond?

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[YueHaohaohao]

I have a similar error.

last line: Computing alignments... cp: '/home/yuehao/seq/AOMDA02.diamond' 与'./AOMDA02.diamond' 为同一文件

The .diamond files and results file are empty.

The problem persists after moving the diamond program to another location.

Is there any way to solve this? Thanks so much for your help!

[pylone-w]

I also encountered the same problem as mentioned above. After running four samples, everything seemed to be normal, but in the end, the same prompt popped up and the tsv output file could not be found in the output folder.

cp: "./nucleotide_seq_04.diamond" and "./nucleotide_seq_04.diamond" are the same file.

[pylone-w]

I solved the above problem and the key issue was caused by file directory. The input file cannot be placed in the NCyc-master directory as it will result in an error: cp: "./nucleotide_seq_.diamond" and "./nucleotide_seq_.diamond" are the same file. The fasta file needs to be placed in another folder and specified it's location using -d <workdir>. I hope this can provide some help for future users and also hope that the author can make relevant modifications to the PL file.