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qichao1984 / NCyc

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No diamond/usearch/blast files were detected! #5

Open amansgill opened 5 years ago

amansgill commented 5 years ago

Hi, I attempted to run NCycProfiler.PL as follows:

$ perl NCycProfiler.PL -d ~/data/ -m /usr/bin/usearch -f fq -s nucl -si sample_info.txt -o NCyc_output
No diamond/usearch/blast files were detected!

What usearch files is the script trying to detect? I thought the script is intended to run usearch against the provided faa.gz files. Am I supposed to run usearch (or diamond or blast) on my selected faa.gz file before running the script, ie is the script looking for the output of a usearch run?

Here are some details on my usearch version, sample info file and read files

$ /usr/bin/usearch10
usearch v10.0.240_i86linux64, 65.6Gb RAM, 32 cores
(C) Copyright 2013-17 Robert C. Edgar, all rights reserved.                            http://drive5.com/usearch

License: [redacted], non-profit use, max 1 process(es)

$ head -2 sample_info.txt
17      2608559
18      325473

$ ls data/ | head -2
17.fq
18.fq

EDIT: updated usearch location and version info

qichao1984 commented 5 years ago

Hello, here are a few tips for you:

  1. uncompress *.faa.gz files, they are gzipped because github does not accept large files.
  2. modify your command to -m usearch, and specify the path of usearch at line 13 of the script. the profiler should work after these.

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From: Aman S. Gill notifications@github.com Sent: Friday, March 22, 2019 4:11:35 AM To: qichao1984/NCyc Cc: Subscribed Subject: [qichao1984/NCyc] No diamond/usearch/blast files were detected! (#5)

Hi, I attempted to run NCycProfiler.PL as follows:

$ perl NCycProfiler.PL -d ~/data/ -m /usr/local/src/usearch -f fq -s nucl -si sample_info.txt -o NCyc_output No diamond/usearch/blast files were detected!

What usearch files is the script trying to detect? I thought the script is intended to run usearch against the provided faa.gz files. Am I supposed to run usearch (or diamond or blast) on my selected faa.gz file before running the script, ie is the script looking for the output of a usearch run?

Here are some details on my sample info file and read files

$ head -2 sample_info.txt 17 2608559 18 325473

$ ls data/ | head -2 17.fq 18.fq

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/qichao1984/NCyc/issues/5, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFromBlPo9ZSjUsL_Q3Ovwvgy2_YetUNks5vY-d3gaJpZM4cCRwg.

avlisaidualc commented 3 years ago

Hello,

I am using NCycProfiler according to description to identify the N cycle genes in MAGs. First, I am testing it on one MAG (1 fasta file) with diamond and the same error here reported is occurring. I've already altered the diamond path in the original script (NCycProfiler.PL), as you recommended, but the error still occurs. I attach the script I am using for checking. error_no diamond files .docx

Do you have any other suggestion to solve this issue? It really would help me a lot with my project, as I have 99 MAGs to analyse... Thanks!

qichao1984 commented 3 years ago

There are a few issues should be paid attention:

  1. The option -rs should be followed by the number of sequences, e.g. -rs 100000

  2. The main issue here is no diamond file is generated: (1) You may check if the diamond program is executable. (2) There should be several lines of diamond running status output on screen.

发件人: @.> 发送时间: 2021年9月8日 23:09 收件人: @.> 抄送: Qichao @.>; @.> 主题: Re: [qichao1984/NCyc] No diamond/usearch/blast files were detected! (#5)

Hello,

I am using NCycProfiler according to description to identify the N cycle genes in MAGs. First, I am testing it on one MAG (1 fasta file) with diamond and the same error here reported is occurring. I've already altered the diamond path in the original script (NCycProfiler.PL), as you recommended, but the error still occurs. I attach the script I am using for checking. error_no diamond files .docxhttps://github.com/qichao1984/NCyc/files/7129908/error_no.diamond.files.docx

Do you have any other suggestion to solve this issue? It really would help me a lot with my project, as I have 99 MAGs to analyse... Thanks!

― You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/qichao1984/NCyc/issues/5#issuecomment-915324309, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNORGG7TRJ2B5YZXHQM2DTUA54BZANCNFSM4HAJDQQA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

avlisaidualc commented 3 years ago

Hello, After many attempts, I correct the path for diamond in NCycProfiler.PL and then finally solve the problem of the data files by decompressing them with keka (using MacOSX). Thanks for your help!