Installation Errors following "Earl Grey Installation and Configuration (If you already have RepeatMasker and RepeatModeler)"

[ufaroooq]

I am following the part "Earl Grey Installation and Configuration (If you already have RepeatMasker and RepeatModeler)".

All the requirments are already installed. RepeatMasker and RepeatMOdeler are installed, configured, and in PATH. While installing EarlGrey by clonign the git repo i am facing some issues.

1. in configure file, the environment name is mentioned as "earlGrey" but when environment is created by the earlGery.yaml file (line 24), it is named as "earlgrey" which raised error as on line 28 which tries to find environment "earlGrey" again. This is due to environment name being "earlgrey" in earlGrey.yaml file line 1. So, I changed the name: earlgrey => name: earlGrey in line 1 of earlGrey.yaml

This worked and configration runs untill line 51. here is the second error.

2. in file configure, line 58 in command after clonning the SA-SSR from git clone https://github.com/ridgelab/SA-SSR sed -i "s|PREFIX=/usr/local/bin|PREFIX=${SCRIPT_DIR}|g" Makefile && make && make install

i get the following errors and all process stops,

make: Warning: File 'Makefile' has modification time 5.9 s in the future
/scratch/miniconda_envs/earlGrey/bin/x86_64-conda-linux-gnu-c++ -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch/miniconda_envs/earlGrey/include -g -Wall -Wextra -std=c++11 -pthread -pedantic -c src/OutputFile.cpp -o obj/OutputFile.o
src/OutputFile.cpp: In member function 'void OutputFile::writeHeaders(const std::vector<std::__cxx11::basic_string<char> >&)':
src/OutputFile.cpp:109:14: error: 'uint32_t' was not declared in this scope
  109 |         for (uint32_t i = 0; i < headers.size(); i++)
      |              ^~~~~~~~
src/OutputFile.cpp:7:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
    6 | #include "../include/OutputFile.h"
  +++ |+#include <cstdint>
    7 |
src/OutputFile.cpp:109:30: error: 'i' was not declared in this scope
  109 |         for (uint32_t i = 0; i < headers.size(); i++)
      |                              ^
src/OutputFile.cpp: In member function 'OutputFile& OutputFile::write(const std::vector<std::__cxx11::basic_string<char> >&)':
src/OutputFile.cpp:136:14: error: 'uint32_t' was not declared in this scope
  136 |         for (uint32_t i = 0; i < output.size(); i++)
      |              ^~~~~~~~
src/OutputFile.cpp:136:14: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
src/OutputFile.cpp:136:30: error: 'i' was not declared in this scope
  136 |         for (uint32_t i = 0; i < output.size(); i++)
      |                              ^
make: *** [Makefile:26: obj/OutputFile.o] Error 1
(/scratch/miniconda_envs/earlGrey) ufarooq@vmepi01:~/tools/EarlGrey/scripts/SA-SSR$

After this when running EarlGrey via command (environment is already activated) ./earlGrey -g genome.fna -s Fusarium -o 47514-EarlGrey/ -t 32

i get the following on terminal.

              )  (
             (   ) )
             ) ( (
           _______)_
        .-'---------|
       ( C|/\/\/\/\/|
        '-./\/\/\/\/|
         '_________'
          '-------'
        <<< Checking Parameters >>>
32 Cores Will Be Used
RepeatMasker species not specified, running Earl Grey without an initial mask with known repeats
De Novo Sequences Will Be Extended Through a Maximum of 10 Iterations
20 sequences will be used in BEAT consensus generation
TE library consensus sequences will not be clustered
Softmasked genome will not be generated
Short TE sequences <100bp will not be removed from annotation
Blast, Extract, Extend, Trim Process Will Add 1000bp to Each End in Each Iteration
Conda environment is inactive, please activate conda environment before using Earl Grey

Kindly assist with the following.

[TobyBaril]

Hi, In this case it looks like your system has an issue with the installation of SA-SSR. This is an older program that is not maintained any longer. This error can sometimes occur if the incorrect compiler for your system is used by make, but the root cause is not easy to find.

In your case, I would recommend installing earl grey using the preconifgured conda package, as this is our main supported version. Install this in a clean conda environment:

conda env remove -n earlgrey

conda create -n earlgrey bioconda::earlgrey

[ufaroooq]

I already tried fresh installation via conda and it worked. Thanks for clearing out the issues.