ERROR: An error occurred, ***please review the error messages*** they may contain useful information about the problem

[gouwei1]

Hi,

I ran orthofinder with 3 species' protein sequence files using a linux colony. After a while, it stopped with the error: ''ERROR: An error occurred, please review the error messages they may contain useful information about the problem''. However, I can not find any more messages and the logfile did not contain useful information as the error said. I've retried many times, showing the same error messages.

The command I typed: orthofinder -t 10 -f /datapool/1.result/orthofinder/pep
The version used: 2.5.4 from conda
The files produced in the WorkingDirectory : (no files produced in the directory of ./pickle)
total 358M
45194105602 8.0K drwxr-xr-x 20 xxxx xxxx 8.0K Mar 3 16:18 .
70921185282 8.0K drwxr-xr-x 4 xxxx xxxx 8.0K Mar 3 15:23 ..
27488497153 14M -rw-r--r-- 1 xxxx xxxx 14M Mar 3 16:18 Blast0_0.txt.gz
67481059330 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:02 Blast0_1.txt.gz
30652224002 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:02 Blast0_2.txt.gz
41956752386 12M -rw-r--r-- 1 xxxx xxxx 12M Mar 3 16:05 Blast1_0.txt.gz
58622755841 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:16 Blast1_1.txt.gz
58520308481 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:12 Blast1_2.txt.gz
65992111618 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:03 Blast2_0.txt.gz
52455502593 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:14 Blast2_1.txt.gz
56561155585 13M -rw-r--r-- 1 xxxx xxxx 13M Mar 3 16:16 Blast2_2.txt.gz
55437562369 42M -rw-r--r-- 1 xxxx xxxx 42M Mar 3 15:23 diamondDBSpecies0.dmnd
73949990402 40M -rw-r--r-- 1 xxxx xxxx 40M Mar 3 15:23 diamondDBSpecies1.dmnd
71371736066 40M -rw-r--r-- 1 xxxx xxxx 40M Mar 3 15:23 diamondDBSpecies2.dmnd
74169331458 4.0K drwxr-xr-x 2 xxxx xxxx 4.0K Mar 3 16:18 pickle
65914660354 6.8M -rw-r--r-- 1 xxxx xxxx 6.8M Mar 3 15:23 SequenceIDs.txt
41745365250 40M -rw-r--r-- 1 xxxx xxxx 40M Mar 3 15:23 Species0.fa
28102683649 38M -rw-r--r-- 1 xxxx xxxx 38M Mar 3 15:23 Species1.fa
27726822913 39M -rw-r--r-- 1 xxxx xxxx 39M Mar 3 15:23 Species2.fa
55740175361 0 -rw-r--r-- 1 xxxx xxxx 69 Mar 3 15:23 SpeciesIDs.txt

Thanks a lot in advance for your help.
Here are the complete messages it shows:

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-03-03 15:23:21 : Starting OrthoFinder 2.5.4
10 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok
Test can run "fastme -i /datapool/1.result/orthofinder/pep/OrthoFinder/Results_Mar03/WorkingDirectory/SimpleTest.phy -o /datapool/1.result/orthofinder/pep/OrthoFinder/Results_Mar03/WorkingDirectory/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing

2022-03-03 15:23:32 : Creating diamond database 1 of 3
2022-03-03 15:23:34 : Creating diamond database 2 of 3
2022-03-03 15:23:36 : Creating diamond database 3 of 3

Running diamond all-versus-all

Using 10 thread(s)
2022-03-03 15:23:38 : This may take some time....
2022-03-03 15:23:38 : Done 0 of 9
2022-03-03 16:18:33 : Done all-versus-all sequence search

Running OrthoFinder algorithm

2022-03-03 16:18:35 : Initial processing of each species
ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

[davidemms]

I've committed a change that should report what the error is. Conda will have already installed orthofinder's dependencies for you so if you download the latest version of the code from github

git clone https://github.com/davidemms/OrthoFinder.git 

and then run that version of the code while still in the conda environment

python OrthoFinder/orthofinder.py

then you should hopefully get a useful error message.

Thanks for reporting this, let me know how you get on.

Best wishes
David

[gouwei1]

Dear David,

Thanks for your reply. The error messages can be seen now:

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-03-09 09:02:01 : Starting OrthoFinder 2.5.4
20 thread(s) for highly parallel tasks (BLAST searches etc.)
2 thread(s) for OrthoFinder algorithm

Checking required programs are installed

ERROR: Cannot run diamond
Format of make database command:
diamond makedb --ignore-warnings --in INPUT -d OUTPUT
ERROR: Cannot run diamond
Format of search database command:
diamond blastp --ignore-warnings -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1
Please check diamond is installed and that the executables are in the system path

ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

It seems diamond is not installed in the conda environment. But when I typed ''diamond help'' directly, it can work normally. I'm wondering if the error is from the Linux cluster (CentOS release 6.8 (Final)) using PBS (Protable Batch System) to submit the task, because there was no error when I used orthofinder (latest installed from conda) on my own laptop (windows subsystem for Linux, Ubuntu 20.04 LTS).

Yours,
Wei