I am having some trouble getting started with Lep-MAP3. I have two families that are a result of reciprocal crosses, each family has 2 F0 parents and 92 F1 offpsring. I plan to create separate linkage maps for the two families, but I did call genotypes from a catalog of loci from all four parents, so I'm hoping the resulting linkage maps will be comparable.
First, how do I generate a pedigree file with my data? I started with a JoinMap input file (generated with Stacks), which I then converted to a linkage file and a post file. Here is the post file for one of the families:
I was also wondering whether I would be able to use the ParentCall2 module if I don't know the sex of the offspring, and if not, would I just start the pipeline with the Filtering2 module?
Thanks so much!
Maria
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You could and should use ParentCall2 even in this case. However, as there are no genotype likelihoods in your data, ParentCall2 wont be as efficient as it could be.
Your input file seems almost correct. However, the first 4 lines seems to have 48637 columns and the remaining 48636. Please check this. If you are using the scripts coming with LM2, please try using dos2unix (or mac2unix) on the loc files, many times they have helped me with similar problems.
And finally, you have to transpose the post file, I tried this (but it did not work because of inconsistent column numbers)
Thanks again! Sorry for the deleted post - I meant to repost my new problem. I managed to get my data through the SeparateChromosomes module, but now I'm stuck at the JoinSingles stage. Here is what my output looks like:
java JoinSingles2 map=PJmap5.txt data=out_PJ.linkage lodLimit=4 numThreads=20
Loading file
No grandparents present in family 1
Number of individuals = 140
Number of families = 1
File loaded with 79743 SNPs
Number of individuals = 140 excluding grandparents
Number of families = 1
Exception in thread "main" java.lang.NumberFormatException: For input string: "Loading"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at LGMap2.loadLGMap(LGMap2.java:191)
at JoinSingles2All.main(JoinSingles2All.java:70)
Do you know what could be causing this error?
Cheers,
Maria
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You seem to have string "Loading" in your map file. Maybe you have directed the error stream in your map file PJmap5.txt? This file should contain only numeric values.
Cheers,
Pasi
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Hi Pasi，
I got the problem,
I use 'nohup' for 'OrderMarkers2', this made some Process information add to the final file, after delete these information, LMPlot run.
Thank you for your reply.
Cheers,
Felix
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Hi Pasi,
I am having some trouble getting started with Lep-MAP3. I have two families that are a result of reciprocal crosses, each family has 2 F0 parents and 92 F1 offpsring. I plan to create separate linkage maps for the two families, but I did call genotypes from a catalog of loci from all four parents, so I'm hoping the resulting linkage maps will be comparable.
First, how do I generate a pedigree file with my data? I started with a JoinMap input file (generated with Stacks), which I then converted to a linkage file and a post file. Here is the post file for one of the families:
https://www.dropbox.com/s/dw9hsfol8et7b3r/JP.post.zip?dl=0
I was also wondering whether I would be able to use the ParentCall2 module if I don't know the sex of the offspring, and if not, would I just start the pipeline with the Filtering2 module?
Thanks so much!
Maria
Dear Maria,
Thank you for your question.
You could and should use ParentCall2 even in this case. However, as there are no genotype likelihoods in your data, ParentCall2 wont be as efficient as it could be.
Your input file seems almost correct. However, the first 4 lines seems to have 48637 columns and the remaining 48636. Please check this. If you are using the scripts coming with LM2, please try using dos2unix (or mac2unix) on the loc files, many times they have helped me with similar problems.
And finally, you have to transpose the post file, I tried this (but it did not work because of inconsistent column numbers)
Cheers,
Pasi
Last edit: Maria Akopyan 2018-08-22
Dear Maria,
Hope you managed to fix the problem.
Cheers,
Pasi
Dear Pasi,
Thanks again! Sorry for the deleted post - I meant to repost my new problem. I managed to get my data through the SeparateChromosomes module, but now I'm stuck at the JoinSingles stage. Here is what my output looks like:
java JoinSingles2 map=PJmap5.txt data=out_PJ.linkage lodLimit=4 numThreads=20
Loading file
No grandparents present in family 1
Number of individuals = 140
Number of families = 1
File loaded with 79743 SNPs
Number of individuals = 140 excluding grandparents
Number of families = 1
Exception in thread "main" java.lang.NumberFormatException: For input string: "Loading"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at LGMap2.loadLGMap(LGMap2.java:191)
at JoinSingles2All.main(JoinSingles2All.java:70)
Do you know what could be causing this error?
Cheers,
Maria
Dear Maria,
You seem to have string "Loading" in your map file. Maybe you have directed the error stream in your map file PJmap5.txt? This file should contain only numeric values.
Cheers,
Pasi
Hi Pasi,
I have a same problem in LMPlot,
java -cp /home/share_data1/lvchf/software/lepmap/bin/ LMPlot order3.txt > order1.dot
java.lang.NegativeArraySizeException
at LMPlot.loadPrints(LMPlot.java:171)
at LMPlot.main(LMPlot.java:301)
I have about 20000makers, do you kown what could be causing this error?
Hi Felix,
Could you send a few lines (head) of the order3.txt. I can figure out the problem faster this way.
Cheers,
Pasi
Hi Pasi,
This is the order3.txt, thank you for your help!
#java OrderMarkers2 map = maplod5size150.txt data = data.call chromosome = 1 numThreads = 20 useKosambi=1 numMergeIterations=1 randSeed=-5037844475770721480
Loading file
No grandparents present in family F
Number of individuals = 82
Number of families = 1
File loaded with 42686 SNPs
Number of individuals = 82 excluding grandparents
Number of families = 1
Number of LGs = 1
Number of markers = 24176
Setting dataScale to 0.0033090668431502318 all likelihoods will be multiplied by 302.2
Initial score = -2314801.915584639
Iteration 1 of 1
884884288488421 done
Polishing map...
score = -566076.9706997629
score = -565725.8202005556
score = -573129.916362328
score = -572770.8962848465
Final score = -565725.8202005556
Setting dataScale to 0.0033090668431502318 all likelihoods will be multiplied by 302.2
Warning: Inconsistencies in phasing, please try using randomPhase=1 and/or hyperPhaser=1 in OrderMarkers2
logL = -565722.6691062748
number of recombinations = 179.0 logL = -565722.6691062748
Individual F 1_1 recombines 4 times
Individual F 1_10 recombines 2 times
Individual F 1_11 recombines 2 times
Individual F 1_12 recombines 4 times
Individual F 1_13 recombines 2 times
.
.
.
Individual F 1_88 recombines 2 times
Individual F 1_9 recombines 3 times
# LG = 1 likelihood = -565722.6691
#marker_number male_position *female_position ( 0.0 )[ phased data] **
38067 0 0 0 1111001110111110001011000100001011100101101101111111100110010100101101101001101000111100100000110001001100011101100111100010100000000111011000100010100101100100 0 0
37814 2.502 0 0 1111001110111110001011000100001011100101100101111111100110010101101101101001101000111100100000110001001100011101100111100010100000000111011000100010100101100100 2 0
32582 6.259 0 0 1111001100111100001011001100001011100101100101111111100110010101101101101001101000111100100000110001001100011101100111100010100000000111011000100010100101100100 3 0
12417 7.509 2.502 0 1111001100111100001011001100001011100001100101111111100110010101101101101001101000111100100000110101001100011101100111100010110000000111011000100010100101100100 1 2
29127 7.509 2.502 0 1111001100111100001011001100001011100001100101111111100110010101101101101001101000111100100000110101001100011101100111100010110000000111011000100010100101100100 0 0
27527 7.509 2.502 0 1111001100111100001011001100001011100001100101111111100110010101101101101001101000111100100000110101001100011101100111100010110000000111011000100010100101100100 0 0
35232 8.76 2.502 0 1111001100111100001011001100001011100001100101111111100110010101100101101001101000111100100000110101001100011101100111100010110000000111011000100010100101100100 1 0
33060 8.76 2.502 0 1111001100111100001011001100001011100001100101111111100110010101100101101001101000111100100000110101001100011101100111100010110000000111011000100010100101100100 0 0
.
.
.
Hi Pasi，
I got the problem,
I use 'nohup' for 'OrderMarkers2', this made some Process information add to the final file, after delete these information, LMPlot run.
Thank you for your reply.
Cheers,
Felix