Open plumbwj01 opened 7 years ago
JFsanchezherrero
commented
7 years ago Dear user, I wonder if you could send us the commandline logfile or any other error files generated by DOMINO in the output folder. It will give us a better understanding on what is going on.
Thank you very much Jose F
plumbwj01
commented
7 years ago Hi Jose, I have attached the generated command line log file, along with both msa (phylip and fa) file formats of the same seq data, as well as images of the stages that I am stuck at. The second and third images display the no taxa issue I am having with both of the suggested file formats (picture 2 being the fa and 3 being the phylip). I don't whether the taxa selection stage is actually essential for DOMINO to function or that I am just interrupting and stopping the scan prematurely when I have selected the files tab to obtain the dm command line file. Sorry for the hassle and thanks again in advance, Will
[image: Inline image 1] [image: Inline image 2] [image: Inline image 3]
On Thu, Sep 28, 2017 at 9:06 AM, Jose Francisco Sanchez-Herrero < notifications@github.com> wrote:
Dear user, I wonder if you could send us the commandline logfile or any other error files generated by DOMINO in the output folder. It will give us a better understanding on what is going on.
Thank you very much Jose F
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###################################################### Project Directory: /Users/user/Desktop/TREES Command line Instruction: /usr/bin/perl /Applications/DOMINO-1.0.1/bin/scripts/DM_Clean_v1.0.0.pl -input_file /Applications/DOMINO-1.0.1/example/I_brauni098.fastq -type_file 5 -l 70 -s 20 -m 100 -p 2 -outputFolder /Users/user/Desktop/TREES -TempFiles
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###################################################### Project Directory: /Users/user/Desktop/TREES Command line Instruction: /usr/bin/perl /Applications/DOMINO-1.0.1/bin/scripts/DM_Assembly_v1.0.0.pl -o /Users/user/Desktop/TREES -mrs 80 -type_file 5 -p 2 -TempFiles
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###################################################### Project Directory: /Users/user/Desktop/TREES Command line Instruction: /usr/bin/perl /Applications/DOMINO-1.0.1/bin/scripts/DM_Clean_v1.0.0.pl -input_file /Users/user/Desktop/TREES/untitled folder/OG70_full_length_guidance_results_full_length_MUSCLE.MSA.MUSCLE.Without_low_SP_Col.With_Names.fasta -type_file 4 -l 70 -s 20 -m 100 -p 2 -outputFolder /Users/user/Desktop/TREES -b /Users/user/Desktop/TREES/untitled folder 2/OG70_CDS_guidance_results_CDS_MUSCLE.MSA.MUSCLE.Without_low_SP_Col.With_Names.fasta
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###################################################### Project Directory: /Users/user/Desktop/TREES Command line Instruction: /usr/bin/perl /Applications/DOMINO-1.0.1/bin/scripts/DM_Assembly_v1.0.0.pl -o /Users/user/Desktop/TREES -mrs 80 -type_file 5 -p 2
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###################################################### Project Directory: /Users/user/Desktop/TREES Command line Instruction: /usr/bin/perl //scripts/DM_MarkerScan_v1.0.0.pl -o /Users/user/Desktop/TREES -VD 0.01 -p 2 -option msa_alignment -msa_file /Users/user/Desktop/output/test.fa -DM selection
######################################################
###################################################### Project Directory: /Users/user/Desktop/TREES Command line Instruction: /usr/bin/perl //scripts/DM_MarkerScan_v1.0.0.pl -o /Users/user/Desktop/TREES -VD 0.01 -p 2 -option msa_alignment -msa_file /Users/user/Desktop/output/test.fa -option msa_alignment -msa_file /Users/user/Desktop/sample.phylip -DM selection
######################################################
CristinaFriasLopez
commented
7 years ago Hi Will,
We are looking for the reason that you got this error.
From while, Please Could you repeat the analysis with our test of msa file (example_phylip.tx) ? You can find it in the following link: https://github.com/molevol-ub/DOMINO/blob/master/example/phylip_msa/example_phylip.txt
Thanks in advance, Cristina
plumbwj01
commented
7 years ago Hello again,
So I am experiencing the same problem with the provided example file. So in response to this I uninstalled and reinstalled both domino and xcode several times to ensure the issue did not lie there; however, this has been to no avail and am still unable to select taxa for the analysis for both the example file and my own data set. I was wondering if the problem could be attributed to human error on my side such as missing a vital step during my attempts to carry out the analysis? Thanks again
On Fri, Sep 29, 2017 at 6:06 PM, CristinaFriasLopez < notifications@github.com> wrote:
Hi Will,
We are looking for the reason that you got this error.
From while, Please Could you repeat the analysis with our test of msa file (example_phylip.tx) ? You can find it in the following link: https://github.com/molevol-ub/DOMINO/blob/master/example/ phylip_msa/example_phylip.txt
Thanks in advance, Cristina
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Dear developers, I am trying to use DOMINO to identify mapping regions which can be used as unique identifiers for several different species of trees. Someone within my group has already generated Multiple sequence alignments for each of the genes of interest, so I have been trying to use the custom run option to bypass the initial stages and starting at "Mapping/Alignment" but I have found when I get to the "marker discovery/selection" stage it displays no selectable taxa and prevents any advancements from that point. I was wondering if you would know of a solution to this problem?
I am using the MSA files in the phylip format and I have attached some example data below just in case the error lies there. Thanks in advance.
3 8807 Taxon1 ---------- -----AGAGA AATGGAGCCA AGAAAAGCAA TAGATGAATT Taxon2 ---------- ---------- -ATGGA---C GAAAAATCGG TGGACGATAA Taxon3 AAACAGATAG CCTGA----- -ATGGAGCCA GGGCTATCAA TCGAAGATCA