No errors were reported, and the program stopped after running for a while

[zzzzzzzy7]

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

[JiaB-He]

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 #

                         #   #
            ###############################
            #                             #
            # 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

[Kalang-Kailang]

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 # # # # # ############################### # # # 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

The same situation also happened to me. Hello, have you solved this? Many thanks!