JiaB-He
commented
9 months ago This situation also happened to me. There was no error message, only intermediate results. Have you solved it now?
Below are all my logs：
Nucmer alignment of genomes, filtering and converting to coordinates
My what a large genome you have, this may take some time #
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# MUM&Co is open for business #
# version 3.8 #
##################################################################################################################################### USING GLOBAL ALIGNMENT COORDINATES FOR DELETIONS, INSERTIONS AND TRANSLOCATIONS ######################################################################################################
Matching query and reference chromosomes
Finding alignment gaps
Filtering for size labelling SV
Finding translocation fragments
Checking alignment sense for inversions involving majority of single chromosome bases
###################################################################################################### USING NON-GLOBAL ALIGNMENT FOR INVERSIONS, DUPLICATIONS AND CONTRACTIONS ######################################################################################################
Matching chromosomes based on names, using '_' seperator and filtering chrMT
Looking for interchromosomal changes in alignment sense, filtering for 1kb fragments and merging closely neighbouring calls
Locating alignment overlaps for duplication assignment
Locating alignment overlaps for contraction assignment
############################################################################################################## Combining both deletions, insertion, inversions and duplications and identifying regions of more than one call ##############################################################################################################
Filtering clean inversions using deletion and insertion information
Combining all called SVs
Removing deletions and insertions called during global alignment due to inversions
Extracting DNA involved in SV events
Hello！I runed this code
bash /Bio_data/zzy/software/MUMandCo/mumandco_v3.8.sh -r common_carp.genome.chr.fin.fasta -q C.auratus.chromosome.chr.fasta -g 1531013968 -t 10 -o sv.But after running it for a while, it ended automatically,and a bunch of intermediate files were exported. I checked the log file and there was nothing wrong.I also uploaded my log file.The same thing happened when I added the -b.Do you know what the problem is?Thank you very much! mumandco.log