cmayer
commented
1 year ago The problem is that the exonerate program crashed. Our experience is that a common reason for this problem is that the computer has insufficient RAM to run exonerate. Can you monitor the RAM while MitoGeneExtractor is running and/or try to use computer with more RAM.
We could also try to analyse the data on one of our machines to find the cause of the problem.
This issue was posted originally by the user avvypaks in the thread of the issue "command not found: MitoGeneExtractor".
Welcome to the MitoGeneExtractor program, version 1.9.5 WARNING: You did not specify a vulgar file, so a temporary vulgar file will be created for this run that will be removed at the end of this program run. Therefor the vulgar file cannot be reused in other runs. Parameter settings:
DNA fastq input file names: merged18.fastq Protein reference input file name: F04translated.fasta Directory for temporary files: . Base name for alignment output file: out-alignment.fas Vulgar file name: tmp-vulgar.txt Genetic code (NCBI genetic code number): 5 Print this number of bp beyond Exonerate alignment: 0 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: 1 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_ZO3Ugq The specified vulgar file exists, so it does not have to be recomputed with exonerate. NOTE: Exonerate hit skipped due to low relative alignment score: 0.792982 396580ee-63da-4195-b01f-1cf01fcfc00f NOTE: Exonerate hit skipped due to low relative alignment score: 0.764368 386f9be3-37d4-40d4-bbb7-6dd7d3ab8eb9 NOTE: Exonerate hit skipped due to low relative alignment score: 0.984848 63ade953-ffdf-4140-8a95-99fd8d23257c WARNING: Vulgar file is incomplete. It does not end with "-- completed exonerate analysis" This is attempt number 1 to read the vulgar file. I will try to recompute the vulgar file. sh: line 1: 15994 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 15999 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16001 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16003 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16009 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16013 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16015 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16017 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16021 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log sh: line 1: 16025 Segmentation fault: 11 exonerate --geneticcode FFLLSSSSYYCCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG --frameshift -9 --query F04translated.fasta -Q protein --target ./Concatenated_exonerate_input_ZO3Ugq -T dna --model protein2dna --showalignment 0 --showvulgar 1 > tmp-vulgar.txt 2> tmp-vulgar.txt.log ERROR: Running exonerate failed. The generated vulgar file is incomplete and should be removed manually. Exiting.
MitoGeneExtractor says goodbye.
IT WOULD BE GREAT IF YOU CAN TELL ME WHAT THIS "Segmentation fault: 11" IS ALL ABOUT.
Originally posted by @avvypaks in https://github.com/cmayer/MitoGeneExtractor/issues/4#issuecomment-1577209112