diamond error "Please specify the location of diamond! at NCycProfiler.PL line 42."

[lluisbertrans]

I write your codes as following:
perl NCycProfiler.PL -d /home/lbertrans/ -m diamond -f fastq -s nucl -si Sequences_samples -o N_genes

The error is:
Please specify the location of diamond! at NCycProfiler.PL line 42.

I changed the path line 11:
my $diamond = "~/home/spack/opt/spack/linux-centos7-broadwell/gcc-4.9.4/diamond-2.0.11-obtc4vtc4dbd7irps2tz2jxstc4icaq5/bin/diamond"

It didn't work. I had the same error as before.

We are working in cluster server. Could it be the access to diamond software?

Thanks.

Lluís

[qichao1984]

Not sure about the path in your system, but you may need to delete the ~ symbol.

…

Sent from my iPhone On Mar 24, 2023, at 00:49, lluisbertrans ***@***.***> wrote:  I write your codes as following: perl NCycProfiler.PL -d /home/lbertrans/ -m diamond -f fastq -s nucl -si Sequences_samples -o N_genes The error is: Please specify the location of diamond! at NCycProfiler.PL line 42. I changed the path line 11: my $diamond = "~/home/spack/opt/spack/linux-centos7-broadwell/gcc-4.9.4/diamond-2.0.11-obtc4vtc4dbd7irps2tz2jxstc4icaq5/bin/diamond" It didn't work. I had the same error as before. We are working in cluster server. Could it be the access to diamond software? Thanks. Lluís — Reply to this email directly, view it on GitHub<#35>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABNORGFGX4MBSNXN5FX6UM3W5R5KHANCNFSM6AAAAAAWFO5IA4>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lluisbertrans]

We tried without this symbol, without exit. Any other idea? Thanks.

[qichao1984]

Perhaps the following: 1. Make sure the diamond executable file is there. 2. Check if it has list and executable right… If nothing is wrong, put the diamond program somewhere simple, like the folder your data or the perl script locates. So that you can debug the script more easily. 发件人: ***@***.***> 发送时间: 2023年3月24日 16:52 收件人: ***@***.***> 抄送: Qichao ***@***.***>; ***@***.***> 主题: Re: [qichao1984/NCyc] diamond error "Please specify the location of diamond! at NCycProfiler.PL line 42." (Issue #35) We tried without this symbol, without exit. Any other idea? Thanks. ― Reply to this email directly, view it on GitHub<#35 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABNORGFJVN5S62YP5YTFZTDW5VODFANCNFSM6AAAAAAWFO5IA4>. You are receiving this because you commented.Message ID: ***@***.***>

[ZQYYRA]

1.use “which diamond” can get diamond site in your server or computer.
2.In my Linux server, the location of Diamond is "home//miniconda/envs//bin/diamond".
3.Copy the pathway , and change the the site of Diamond in PL filelike this : my $diamond="home//miniconda/envs//bin/diamond".
4.In my experiences, use "~" replace "home/***" will get this error: Please specify the location of diamond! at NCycProfiler.PL line 42.
Hope this messages are helpful for you.