CrossmatchSearchEngine::parseOutput: Unable to open results file

[Anees-caas]

Hi, when I am running the following command RepeatMasker-pa 16 -gff -s -noint -xsmall -nolow -x -e ncbi -lib consensi.fa genome.fasta I am getting following errors CrossmatchSearchEngine::parseOutput: Unable to open results file: /home/ug1985/TEs/repeatmasker/RM_27068.TueJul300849202024/genome.fasta_batch-10.cat : No such file or directory at /home/ug1985/.conda/envs/bioinformatics/bin/RepeatMasker line 4732. CrossmatchSearchEngine::parseOutput: Unable to open results file: /home/ug1985/TEs/repeatmasker/RM_27068.TueJul300849202024/genome.fasta_batch-1.cat : No such file or directory at /home/ug1985/.conda/envs/bioinformatics/bin/RepeatMasker line 4732. (bioinformatics) ug1985@gs63:~/TEs/repeatmasker$ CrossmatchSearchEngine::parseOutput: Unable to open results file: /home/ug1985/TEs/repeatmasker/RM_27068.TueJul300849202024/genome.fasta_batch-13.cat : No such file or directory at /home/ug1985/.conda/envs/bioinformatics/bin/RepeatMasker line 4732. CrossmatchSearchEngine::parseOutput: Unable to open results file: /home/ug1985/TEs/repeatmasker/RM_27068.TueJul300849202024/genome.fasta_batch-15.cat : No su(bioinformatics) ug1985@gs63:~/TEs/repeatmasker$ bioinformatics/bin/RepeatMasker line 4732. However, the command is not ending but it stacked there and not generating and further temporary files.

[rmhubley]

A few things to note from your output. The first is that it appears you are using a conda installation of RepeatMasker. We do not currently support Conda with RepeatMasker as there have been a huge number of issues reported with their recipes. I would recommend installing RepeatMasker from source. It appears that something is going wrong invoking or completing runs of cross_match. Could you verify that cross_match is installed and can be run by hand like so:

% /usr/local/phrap-1.090518/cross_match 

/usr/local/phrap-1.090518/cross_match /usr/local/phrap-1.090518/cross_match 
cross_match version 1.090518

[rmhubley]

I am going to close this, please let us know if you are still having problems.

[Anees-caas]

@rmhubley this problem is solved. you could close it now.