MCScanX
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wyp1125
0 matches imported (0 discarded). No genes detected.
Hi Yupeng, Thanks for making MCScanX available. I'm trying to run the tool on my concatenated blast results and "gff" but I keep getting 0 matches imported and 0 discarded. Am I missing something trivial? My gene ids in blast and "gff" are matching. For my "gff" I've renamed the chromosome column to the "sp#" format as instructed in the manual. I'm not getting any errors either. Tips?
> Reading BLAST file and pre-processing
> Generating BLAST list
> 0 matches imported (0 discarded)
> 0 pairwise comparisons
> 0 alignments generated
> Pairwise collinear blocks written to data/mcscanx/input/.collinearity [0.004 seconds elapsed]
> Writing multiple syntenic blocks to HTML files
> Done! [0.006 seconds elapsed]
.collinearity :
> ############### Parameters ###############
> # MATCH_SCORE: 50
> # MATCH_SIZE: 5
> # GAP_PENALTY: -1
> # OVERLAP_WINDOW: 5
> # E_VALUE: 1e-05
> # MAX GAPS: 25
> ############### Statistics ###############
> # Number of collinear genes: 0, Percentage: -nan
> # Number of all genes: 0
> ##########################################
Thank you for your time :smile:
Hi @ehsueh ,
Did you get MCScanX to work? I am also having issues with the input file format
$ ~/bin/MCScanX/MCScanX inputs_2/test
Reading BLAST file and pre-processing
Generating BLAST list
0 matches imported (24924 discarded)
0 pairwise comparisons
0 alignments generated
I think the issue is in the input files, the scripts run for me. Thanks,
Dario
I am also having the same issue even for the At example files available there. Did you find a solution?
Hi @ehsueh ,
Did you get MCScanX to work? I am also having issues with the input file format
$ ~/bin/MCScanX/MCScanX inputs_2/test Reading BLAST file and pre-processing Generating BLAST list 0 matches imported (24924 discarded) 0 pairwise comparisons 0 alignments generatedI think the issue is in the input files, the scripts run for me. Thanks,
Dario
I am also having the same issue even for the At example files available there. Did you find a solution?
I found the solution (big thanks goes to threesup at reddit. Solution:
Put .blast and .gff files inside MCScanX directory without making a separate folder for the files.
hi,ehsueh I have same problem with you. the protein ID in pep.fa file is same to gene ID in gff. However MCScanX also on results. Could you tell me the solution? Thank you very much !
Hi Yupeng, Thanks for making MCScanX available. I'm trying to run the tool on my concatenated blast results and "gff" but I keep getting 0 matches imported and 0 discarded. Am I missing something trivial? My gene ids in blast and "gff" are matching. For my "gff" I've renamed the chromosome column to the "sp#" format as instructed in the manual. I'm not getting any errors either. Tips?
> Reading BLAST file and pre-processing > Generating BLAST list > 0 matches imported (0 discarded) > 0 pairwise comparisons > 0 alignments generated > Pairwise collinear blocks written to data/mcscanx/input/.collinearity [0.004 seconds elapsed] > Writing multiple syntenic blocks to HTML files > Done! [0.006 seconds elapsed].collinearity :
> ############### Parameters ############### > # MATCH_SCORE: 50 > # MATCH_SIZE: 5 > # GAP_PENALTY: -1 > # OVERLAP_WINDOW: 5 > # E_VALUE: 1e-05 > # MAX GAPS: 25 > ############### Statistics ############### > # Number of collinear genes: 0, Percentage: -nan > # Number of all genes: 0 > ##########################################Thank you for your time 😄
Hi, ehsueh Have you soluted the problem at last? I have the same question with you. Thank you
Hi,
Ive also run into the same problem as the other posters:
./MCScanX LEN2/LEN2 Reading BLAST file and pre-processing Generating BLAST list 0 matches imported (52663 discarded) 0 pairwise comparisons 0 alignments generated Pairwise collinear blocks written to LEN2/LEN2.collinearity [0.336 seconds elapsed] Writing multiple syntenic blocks to HTML files
I've tried the suggested solution of running from the MCScanX folder but that hasn't helped. Has anyone figured out what's going on here? I've checked my input files have the names matching and they are and I've checked the file formats too and all appears to be fine.
Cheers, Chris
I eventually was able to run MCScan, but I don't remember how. I think that one thing that I had wrong was the gff file, since I did not concatenate the two gffs into one. Hoping this helps!
I know it's old, but in case anyone has the same problem (I just did) -- I solved it by making sure that both the .blast and the .gff files were TAB-delimited. I had the "0 matches imported" problem when the .gff file was space-delimited.
The tr command can be used to change it easily:
< file.gff tr ' ' '\t' > file_tab.gff
(left this comment on BioStars too).
Hi, I too was having the issue, and was making a mistake with my GFF formatting.
Initially my output was looking like..
Reading BLAST file and pre-processing
Generating BLAST list
0 matches imported (121824 discarded)
0 pairwise comparisons
0 alignments generated
...
I noticed when comparing the at test data that the GFF file was formatted
chr# gene starting_position ending_position
Where as the GitHub page has the following BED/GFF suggestion, and my GFF was formatted like this.
chr# starting_position ending_position gene
After altering my GFF file, my output looked like this...
Reading BLAST file and pre-processing
Generating BLAST list
96657 matches imported (25167 discarded)
88698 pairwise comparisons
1 alignments generated
Cheers
Hi ! I manage to solve this : First the bed file has to be renames to .gff. Then it has : chr gene start stop Most importantly : the files have to be in the data/ folder of MCscan ! It is not enough to put MCscan folder in your path
Cheers
Hi ! I manage to solve this : First the bed file has to be renames to .gff. Then it has : chr gene start stop Most importantly : the files have to be in the data/ folder of MCscan ! It is not enough to put MCscan folder in your path
Cheers
This + making the files tab delimited worked for me!
