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qichao1984 / NCyc

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Output file not detected #12

Open bishav6708 opened 4 years ago

bishav6708 commented 4 years ago

Hello, I ran the perl script. The script runs till the following message is displayed:

Reported 91 pairwise alignments, 100 HSSPs 91 queries aligned.

3

and terminates

I can't locate my output file. Can you mention where that might be.

Here is my script.

perl NCycProfiler.PL -d ~/prokka/cb2_bin9/ -m diamond -f fa -s nucl -si ~/prokka/cb2_bin9/ncyctry -o out_ncyc

bishav6708 commented 4 years ago

Hello, Can you help me in the above mentioned issue? The program gets aborted with error #3. looking at the perl script, it has something to do with opening the $sampleinfo file.

Bishav

ZehanDai commented 4 years ago

Hello, I ran the perl script. The script runs till the following message is displayed:

Reported 91 pairwise alignments, 100 HSSPs 91 queries aligned.

3

and terminates

I can't locate my output file. Can you mention where that might be.

Here is my script.

perl NCycProfiler.PL -d ~/prokka/cb2_bin9/ -m diamond -f fa -s nucl -si ~/prokka/cb2_bin9/ncyctry -o out_ncyc

Hi~

Have you solved the problem? I had the same issue. The perl scipt seemed to run fine but no output file could be found.

avlisaidualc commented 2 years ago

Hello, I ran the perl script. The script runs till the following message is displayed: Reported 91 pairwise alignments, 100 HSSPs 91 queries aligned.

3

and terminates I can't locate my output file. Can you mention where that might be. Here is my script. perl NCycProfiler.PL -d ~/prokka/cb2_bin9/ -m diamond -f fa -s nucl -si ~/prokka/cb2_bin9/ncyctry -o out_ncyc

Hi~

Have you solved the problem? I had the same issue. The perl scipt seemed to run fine but no output file could be found.

Hello,

Same problem here. How did you solve it? Thanks!

ZehanDai commented 2 years ago

Hello, I ran the perl script. The script runs till the following message is displayed: Reported 91 pairwise alignments, 100 HSSPs 91 queries aligned.

3

and terminates I can't locate my output file. Can you mention where that might be. Here is my script. perl NCycProfiler.PL -d ~/prokka/cb2_bin9/ -m diamond -f fa -s nucl -si ~/prokka/cb2_bin9/ncyctry -o out_ncyc

Hi~ Have you solved the problem? I had the same issue. The perl scipt seemed to run fine but no output file could be found.

Hello,

Same problem here. How did you solve it? Thanks!

Hi, I haven't solved the problem and I moved on to use my own method. I write a shell/python script to run and phase the raw result following the methodology of this script.

The file NCycProfiler.PL is a wrap-up script for running alignment tools, by which you could search your query file against a database. The method you could use include diamond(protein blast), Usearch and blast, with fixed parameters according to this: || $method !~ /^diamond|usearch|blast$/ After running alignment, the gene information was fetched by 'id2gene'. So if you have the basic programming knowledge, you could do it in a similar way, which I strongly suggest.