Running exonerate failed

[ladywaspzhu]

Hi,

I am working on the extraction of mitochondrial genes (mainly for COI) from UCE data. both two fq
file are 3.7 GB, i use the conmmand as follows:
MitoGeneExtractor-v1.9.5 -q AS_aura_YN_1.fq -q AS_aura_YN_2.fq -p COI-consensus.fas -V vulgar.txt -o out-alignment.fas -n 1 -c out-consensus.fas -t 0.5 -r 32 -C 5

However, i got the following errors:
Welcome to the MitoGeneExtractor program, version 1.9.5
Parameter settings:

DNA fastq input file names: AS_aura_YN_1.fq,AS_aura_YN_2.fq
Keep concatenated input file: no
Protein reference input file name: COI-consensus.fas
Directory for temporary files: .
Base name for alignment output file: out-alignment.fas
Vulgar file name: vulgar.txt
Genetic code (NCBI genetic code number): 5
Print this number of bp beyond Exonerate alignment: 1
Write consensus sequence to file : yes
Filename for consensus sequence output: out-consensus.fas
Consensus sequence threshold value: 0.5
Frameshift penalty: -9
Relative score threshold: 32
Minimum coverage in Exonerate alignment: 1
Minimum coverage in Exonerate alignment (upper case): 1
Gappy reads used: yes
Frameshift reads used: no
Treat all references as independent: no
Report gaps mode: Report all (leading, trailing, internal) gaps with '-' character.
Verbosity: 1

Filename:./Concatenated_exonerate_input_XXXXXX
Filename:./Concatenated_exonerate_input_XXXXXX
Filename:./Concatenated_exonerate_input_PM8yLD
No vulgar file with the specified name has been found. So the binary "exonerate" will be used to create the vulgar file.
ERROR: Running exonerate failed. The generated vulgar file is incomplete and should be removed manually. Exiting.

MitoGeneExtractor says goodbye.

I notice that in the closed issue, you mentioned about the memory out of range, and could specify more memory, but i could not find the parameter i can use, or how can i fix these problem?

Thanks a lot

[cmayer]

Hi ladywaspzhu,

since the input file is 3.7 GB large you will need a considerable amount of RAM.
How much RAM do you have and do you have access to a machine with more RAM?

I did consider to modify MGE to split large files into smaller yunks that exonerate can digest.
Exonerate is quite fast but requires a lot of RAM. I will look into this.

Best
Christoph

[ladywaspzhu]

Hi Christoph,

Thanks for replying, i checked the RAM i have and this is the result:

as a non-root, i am not sure whether i can access more RAM, i can have a try. But i do not know how much RMA i need to run the whole file.

Thanks a lot

Warm Regards