WGDdetector
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yongzhiyang2012
new to WGD analysis
Hi,
First of all, thank you so much for creating this pipeline since I was really struggling to do one step at a time to perform WGD. I am new to this part of genome analysis and still working around it to understand better. This tool was easy to install and I was able to run the test run, so, I am assuming that this tool should work (my real data analysis is on-going).
I am curious about the final output of this tool as I am not sure if the test run was complete or achieved what it was supposed to. The fourth folder of test run contained final.ks.distribution.list, so is this the final output. I thought that the final output will be fig2 of the manuscript?
What r-script did you use to generate fig2, simple hist function?
I also got data from https://github.com/yongzhiyang2012/WGDdetector_paper_results. I can see Arabidopsis results and Arabidopsis_thaliana.WGDdetector.final.ks.distribution.list file. Your manuscript showed two peaks for Arabidopsis using this data. I was previously reading Opium poppy genome were authors also performed Ks analysis (but using reciprocal best hit and syntenic analysis approach). When I checked their result, I think they have one peak (please see Fig. S13 from this link- http://science.sciencemag.org/content/sci/suppl/2018/08/29/science.aat4096.DC1/aat4096_Guo_SM.pdf)
There is another tool published this year that uses OrthoMCL results to calculate dS distribution, and their figure4B also showed one peak- https://peerj.com/articles/6303/
I am a little confused as then the interpretation will change, isn't? I know that both methods are not the same, but just curious on your take on this. Reason for asking this silly question is that using your pipeline seems very easy and effective to me, but just wanted to hear from you about these different results to understand the cause behind it.
Looking forward to your reply.
with best regards Amit
- The simple plot Rscript at https://github.com/yongzhiyang2012/WGDdetector/blob/master/src/example.Rscript. The Fig. 2 is using the facet_grid function in ggplot2, you can try it.
- The two paper using the different method to detect the WGD events occured in Opium poppy genome. When only using the reciprocal best hit genes within one species, may losing the ancient WGD signals of th Opium poppy genome. At the same time, you can see the synteny and the gene family results are same.
Thanks for the reply.
I tried running my genome using your tool but kind of stuck in between.
The tool has four steps. I was able to run test without any problem and hence decided to run my data. First step was perfect and I got expected results (clustering info). Next step seems run created files (I opted not to delete temp file to see whats going on) but then program showed error and ended up producing final file with no content in it.
I got these messages while running the program (part of many lines) --------------------- WARNING --------------------- MSG: Jukes Cantor won't work -too divergent!
Use of uninitialized value $Ds in pattern match (m//) at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/calculate_ks.single.pl line 22, <$tmpfh> line 5.
--------------------- WARNING --------------------- MSG: Jukes Cantor won't work -too divergent!
Use of uninitialized value $Ds in pattern match (m//) at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/calculate_ks.single.pl line 22, <$tmpfh> line 5.
--------------------- WARNING --------------------- MSG: Jukes Cantor won't work -too divergent!
Use of uninitialized value $Ds in pattern match (m//) at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/calculate_ks.single.pl line 22, <$tmpfh> line 5.
--------------------- WARNING --------------------- MSG: Jukes Cantor won't work -too divergent!
Use of uninitialized value $Ds in pattern match (m//) at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/calculate_ks.single.pl line 22, <$tmpfh> line 5.
--------------------- WARNING --------------------- MSG: Jukes Cantor won't work -too divergent!
Use of uninitialized value $Ds in pattern match (m//) at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/calculate_ks.single.pl line 22, <$tmpfh> line 5.
--------------------- WARNING --------------------- MSG: Jukes Cantor won't work -too divergent!
Use of uninitialized value $Ds in pattern match (m//) at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/calculate_ks.single.pl line 22, <$tmpfh> line 5.
Towards the end, I got this message- No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. No such file or directory at /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/sub_ks_family.pl line 73. 2019年 2月 19日 火曜日 18:05:58 JST
collecting final ks result for plot and comapring
I think second step finsihed as I can see all output files, but step 3 only have shell script and seems nothing happened.
Please help me.
Please let me know any specific information you need to give me advice on solving this issue.
thank you so much,
with best regards Amit
The warning is OK, it doesn't effect the results. As you menthod the error "No such file or directory at XXX", you can try the test data first to check if all the scripts is right.
I tried test run and no issue. I got all the results as expected and was able to plot. Test run ended very quickly with no problem. Thats why I am not sure where is the error.
In terms of files created in temp at 2nd stage, I have these files- cluster1705.split_0.input.cds.file.align.output.ks.gz cluster1.split_202.input.cds.file cluster1.split_949.input.pep.file cluster2687.split_0.input.cds.file.align cluster433.split_0.input.pep.file.align cluster99.split_0.input.cds.file.align.output.ks.gz cluster1705.split_0.input.pep.file cluster1.split_202.input.cds.file.align cluster1.split_949.input.pep.file.align cluster2687.split_0.input.cds.file.align.output.ks.gz cluster434.split_0.input.cds.file cluster99.split_0.input.pep.file cluster1705.split_0.input.pep.file.align cluster1.split_202.input.cds.file.align.output.ks.gz cluster1.split_94.input.cds.file cluster2687.split_0.input.pep.file cluster434.split_0.input.cds.file.align cluster99.split_0.input.pep.file.align cluster1706.split_0.input.cds.file cluster1.split_202.input.pep.file cluster1.split_94.input.cds.file.align cluster2687.split_0.input.pep.file.align cluster434.split_0.input.cds.file.align.output.ks.gz cluster9.split_0.input.cds.file cluster1706.split_0.input.cds.file.align cluster1.split_202.input.pep.file.align cluster1.split_94.input.cds.file.align.output.ks.gz cluster2688.split_0.input.cds.file cluster434.split_0.input.pep.file cluster9.split_0.input.cds.file.align cluster1706.split_0.input.cds.file.align.output.ks.gz cluster1.split_203.input.cds.file cluster1.split_94.input.pep.file cluster2688.split_0.input.cds.file.align cluster434.split_0.input.pep.file.align cluster9.split_0.input.cds.file.align.output.ks.gz cluster1706.split_0.input.pep.file cluster1.split_203.input.cds.file.align cluster1.split_94.input.pep.file.align cluster2688.split_0.input.cds.file.align.output.ks.gz cluster435.split_0.input.cds.file cluster9.split_0.input.pep.file cluster1706.split_0.input.pep.file.align cluster1.split_203.input.cds.file.align.output.ks.gz cluster1.split_950.input.cds.file cluster2688.split_0.input.pep.file cluster435.split_0.input.cds.file.align cluster9.split_0.input.pep.file.align cluster1707.split_0.input.cds.file cluster1.split_203.input.pep.file cluster1.split_950.input.cds.file.align cluster2688.split_0.input.pep.file.align cluster435.split_0.input.cds.file.align.output.ks.gz cluster9.split_1.input.cds.file cluster1707.split_0.input.cds.file.align cluster1.split_203.input.pep.file.align cluster1.split_950.input.cds.file.align.output.ks.gz cluster2689.split_0.input.cds.file cluster435.split_0.input.pep.file cluster9.split_1.input.cds.file.align cluster1707.split_0.input.cds.file.align.output.ks.gz cluster1.split_204.input.cds.file cluster1.split_950.input.pep.file cluster2689.split_0.input.cds.file.align cluster435.split_0.input.pep.file.align cluster9.split_1.input.cds.file.align.output.ks.gz cluster1707.split_0.input.pep.file cluster1.split_204.input.cds.file.align cluster1.split_950.input.pep.file.align cluster2689.split_0.input.cds.file.align.output.ks.gz cluster436.split_0.input.cds.file cluster9.split_1.input.pep.file cluster1707.split_0.input.pep.file.align cluster1.split_204.input.cds.file.align.output.ks.gz cluster1.split_951.input.cds.file cluster2689.split_0.input.pep.file cluster436.split_0.input.cds.file.align cluster9.split_1.input.pep.file.align cluster1708.split_0.input.cds.file cluster1.split_204.input.pep.file cluster1.split_951.input.cds.file.align cluster2689.split_0.input.pep.file.align cluster436.split_0.input.cds.file.align.output.ks.gz cluster9.split_2.input.cds.file cluster1708.split_0.input.cds.file.align cluster1.split_204.input.pep.file.align cluster1.split_951.input.cds.file.align.output.ks.gz cluster268.split_0.input.cds.file cluster436.split_0.input.pep.file cluster9.split_2.input.cds.file.align cluster1708.split_0.input.cds.file.align.output.ks.gz cluster1.split_205.input.cds.file cluster1.split_951.input.pep.file cluster268.split_0.input.cds.file.align cluster436.split_0.input.pep.file.align cluster9.split_2.input.cds.file.align.output.ks.gz cluster1708.split_0.input.pep.file cluster1.split_205.input.cds.file.align cluster1.split_951.input.pep.file.align cluster268.split_0.input.cds.file.align.output.ks.gz cluster437.split_0.input.cds.file cluster9.split_2.input.pep.file cluster1708.split_0.input.pep.file.align cluster1.split_205.input.cds.file.align.output.ks.gz cluster1.split_952.input.cds.file cluster268.split_0.input.pep.file cluster437.split_0.input.cds.file.align cluster9.split_2.input.pep.file.align cluster1709.split_0.input.cds.file cluster1.split_205.input.pep.file cluster1.split_952.input.cds.file.align cluster268.split_0.input.pep.file.align cluster437.split_0.input.cds.file.align.output.ks.gz cluster9.split_3.input.cds.file cluster1709.split_0.input.cds.file.align cluster1.split_205.input.pep.file.align cluster1.split_952.input.cds.file.align.output.ks.gz cluster2690.split_0.input.cds.file cluster437.split_0.input.pep.file cluster9.split_3.input.cds.file.align cluster1709.split_0.input.cds.file.align.output.ks.gz cluster1.split_206.input.cds.file cluster1.split_952.input.pep.file cluster2690.split_0.input.cds.file.align cluster437.split_0.input.pep.file.align cluster9.split_3.input.cds.file.align.output.ks.gz cluster1709.split_0.input.pep.file cluster1.split_206.input.cds.file.align cluster1.split_952.input.pep.file.align cluster2690.split_0.input.cds.file.align.output.ks.gz cluster438.split_0.input.cds.file cluster9.split_3.input.pep.file cluster1709.split_0.input.pep.file.align cluster1.split_206.input.cds.file.align.output.ks.gz cluster1.split_953.input.cds.file cluster2690.split_0.input.pep.file cluster438.split_0.input.cds.file.align cluster9.split_3.input.pep.file.align cluster170.split_0.input.cds.file cluster1.split_206.input.pep.file cluster1.split_953.input.cds.file.align cluster2690.split_0.input.pep.file.align cluster438.split_0.input.cds.file.align.output.ks.gz cluster9.split_4.input.cds.file cluster170.split_0.input.cds.file.align cluster1.split_206.input.pep.file.align cluster1.split_953.input.cds.file.align.output.ks.gz cluster2691.split_0.input.cds.file cluster438.split_0.input.pep.file cluster9.split_4.input.cds.file.align cluster170.split_0.input.cds.file.align.output.ks.gz cluster1.split_207.input.cds.file cluster1.split_953.input.pep.file cluster2691.split_0.input.cds.file.align cluster438.split_0.input.pep.file.align cluster9.split_4.input.cds.file.align.output.ks.gz cluster170.split_0.input.pep.file cluster1.split_207.input.cds.file.align cluster1.split_953.input.pep.file.align cluster2691.split_0.input.cds.file.align.output.ks.gz cluster439.split_0.input.cds.file cluster9.split_4.input.pep.file cluster170.split_0.input.pep.file.align cluster1.split_207.input.cds.file.align.output.ks.gz cluster1.split_954.input.cds.file cluster2691.split_0.input.pep.file cluster439.split_0.input.cds.file.align cluster9.split_4.input.pep.file.align cluster1710.split_0.input.cds.file cluster1.split_207.input.pep.file cluster1.split_954.input.cds.file.align cluster2691.split_0.input.pep.file.align cluster439.split_0.input.cds.file.align.output.ks.gz cluster9.split_5.input.cds.file cluster1710.split_0.input.cds.file.align cluster1.split_207.input.pep.file.align cluster1.split_954.input.cds.file.align.output.ks.gz cluster2692.split_0.input.cds.file cluster439.split_0.input.pep.file cluster9.split_5.input.cds.file.align cluster1710.split_0.input.cds.file.align.output.ks.gz cluster1.split_208.input.cds.file cluster1.split_954.input.pep.file cluster2692.split_0.input.cds.file.align cluster439.split_0.input.pep.file.align cluster9.split_5.input.cds.file.align.output.ks.gz cluster1710.split_0.input.pep.file cluster1.split_208.input.cds.file.align cluster1.split_954.input.pep.file.align cluster2692.split_0.input.cds.file.align.output.ks.gz cluster43.split_0.input.cds.file cluster9.split_5.input.pep.file cluster1710.split_0.input.pep.file.align cluster1.split_208.input.cds.file.align.output.ks.gz cluster1.split_955.input.cds.file cluster2692.split_0.input.pep.file cluster43.split_0.input.cds.file.align cluster9.split_5.input.pep.file.align cluster1711.split_0.input.cds.file cluster1.split_208.input.pep.file cluster1.split_955.input.cds.file.align cluster2692.split_0.input.pep.file.align cluster43.split_0.input.cds.file.align.output.ks.gz cluster9.split_6.input.cds.file cluster1711.split_0.input.cds.file.align cluster1.split_208.input.pep.file.align cluster1.split_955.input.cds.file.align.output.ks.gz cluster2693.split_0.input.cds.file cluster43.split_0.input.pep.file cluster9.split_6.input.cds.file.align cluster1711.split_0.input.cds.file.align.output.ks.gz cluster1.split_209.input.cds.file cluster1.split_955.input.pep.file cluster2693.split_0.input.cds.file.align cluster43.split_0.input.pep.file.align cluster9.split_6.input.cds.file.align.output.ks.gz cluster1711.split_0.input.pep.file cluster1.split_209.input.cds.file.align cluster1.split_955.input.pep.file.align cluster2693.split_0.input.cds.file.align.output.ks.gz cluster440.split_0.input.cds.file cluster9.split_6.input.pep.file cluster1711.split_0.input.pep.file.align cluster1.split_209.input.cds.file.align.output.ks.gz cluster1.split_956.input.cds.file cluster2693.split_0.input.pep.file cluster440.split_0.input.cds.file.align cluster9.split_6.input.pep.file.align cluster1712.split_0.input.cds.file cluster1.split_209.input.pep.file cluster1.split_956.input.cds.file.align cluster2693.split_0.input.pep.file.align cluster440.split_0.input.cds.file.align.output.ks.gz cluster9.split_7.input.cds.file cluster1712.split_0.input.cds.file.align cluster1.split_209.input.pep.file.align cluster1.split_956.input.cds.file.align.output.ks.gz cluster2694.split_0.input.cds.file cluster440.split_0.input.pep.file cluster9.split_7.input.cds.file.align cluster1712.split_0.input.cds.file.align.output.ks.gz cluster1.split_20.input.cds.file cluster1.split_956.input.pep.file cluster2694.split_0.input.cds.file.align cluster440.split_0.input.pep.file.align cluster9.split_7.input.cds.file.align.output.ks.gz cluster1712.split_0.input.pep.file cluster1.split_20.input.cds.file.align cluster1.split_956.input.pep.file.align cluster2694.split_0.input.cds.file.align.output.ks.gz cluster441.split_0.input.cds.file cluster9.split_7.input.pep.file cluster1712.split_0.input.pep.file.align cluster1.split_20.input.cds.file.align.output.ks.gz cluster1.split_957.input.cds.file cluster2694.split_0.input.pep.file cluster441.split_0.input.cds.file.align cluster9.split_7.input.pep.file.align cluster1713.split_0.input.cds.file cluster1.split_20.input.pep.file cluster1.split_957.input.cds.file.align cluster2694.split_0.input.pep.file.align cluster441.split_0.input.cds.file.align.output.ks.gz cluster9.split_8.input.cds.file cluster1713.split_0.input.cds.file.align cluster1.split_20.input.pep.file.align cluster1.split_957.input.cds.file.align.output.ks.gz cluster2695.split_0.input.cds.file cluster441.split_0.input.pep.file cluster9.split_8.input.cds.file.align cluster1713.split_0.input.cds.file.align.output.ks.gz cluster1.split_210.input.cds.file cluster1.split_957.input.pep.file cluster2695.split_0.input.cds.file.align cluster441.split_0.input.pep.file.align cluster9.split_8.input.cds.file.align.output.ks.gz cluster1713.split_0.input.pep.file cluster1.split_210.input.cds.file.align cluster1.split_957.input.pep.file.align cluster2695.split_0.input.cds.file.align.output.ks.gz cluster442.split_0.input.cds.file cluster9.split_8.input.pep.file cluster1713.split_0.input.pep.file.align cluster1.split_210.input.cds.file.align.output.ks.gz cluster1.split_958.input.cds.file cluster2695.split_0.input.pep.file cluster442.split_0.input.cds.file.align cluster9.split_8.input.pep.file.align cluster1714.split_0.input.cds.file cluster1.split_210.input.pep.file cluster1.split_958.input.cds.file.align cluster2695.split_0.input.pep.file.align cluster442.split_0.input.cds.file.align.output.ks.gz cluster9.split_9.input.cds.file cluster1714.split_0.input.cds.file.align cluster1.split_210.input.pep.file.align cluster1.split_958.input.cds.file.align.output.ks.gz cluster2696.split_0.input.cds.file cluster442.split_0.input.pep.file cluster9.split_9.input.cds.file.align cluster1714.split_0.input.cds.file.align.output.ks.gz cluster1.split_211.input.cds.file cluster1.split_958.input.pep.file cluster2696.split_0.input.cds.file.align cluster442.split_0.input.pep.file.align cluster9.split_9.input.cds.file.align.output.ks.gz cluster1714.split_0.input.pep.file cluster1.split_211.input.cds.file.align cluster1.split_958.input.pep.file.align cluster2696.split_0.input.cds.file.align.output.ks.gz cluster443.split_0.input.cds.file cluster9.split_9.input.pep.file cluster1714.split_0.input.pep.file.align cluster1.split_211.input.cds.file.align.output.ks.gz cluster1.split_959.input.cds.file cluster2696.split_0.input.pep.file cluster443.split_0.input.cds.file.align cluster9.split_9.input.pep.file.align
And for third stage, I have these files- 01.hcluster.all.sh 02.sub_GF.sh 03.two_clad.sh
I do not have cluster folder as I observed in Test run. So, I am not sure what went wrong.
Please help. How can I trouble shoot or what information I should look at?
Hi,
I just did a test run using Arabidopsis data that you used for publication. I just used this command-
perl /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/bin/wgddetector.pl
--input_cds /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/WGDdetector_paper_results/Arabidopsis_thaliana/Arabidopsis_thaliana.clean.cds
--input_pep /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/WGDdetector_paper_results/Arabidopsis_thaliana/Arabidopsis_thaliana.clean.pep
--output_dir /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/WGDdetector_paper_results/Arabidopsis_thaliana/Ara_wgd_18thFEb2019_r1.4
--tmp_dir /mnt/md0/Opu_r1.2_final/Comparitive_genomics/WGDdetector/test_run_temp
--thread_num 64 --cluster_engine mmseqs2
But the program was not successful. I am attaching the logfile. Can you derive any solution through this. arabi_testrun.txt
Thank you so much,
with best regards Amit
Hi there, I'm trying to use the "example.Rscript" to plot the final results and got an error message
Error in FUN(X[[i]], ...) : object 'V3' not found Calls: <Anonymous> ... ggplot_build.ggplot -> by_layer -> f -> <Anonymous> -> f -> lapply -> FUN Execution halted
How to fix that ?
Since I'm not a "R" guy, is really difficult to interpret the final result whitout a good plotting like the provided in the manuscript. Could you release the Rscript used to generate the Fig2 ?
Hi,
I am getting following errors while running WGD. I was not getting these errors while running the test run (00.run.sh), it ran fine and I got both final.ks.distribution.list and final.ks.distribution.list,pdf
Error in read.table("output/02.ks_estimate/ks_martix/cluster477/ks.dist") : first five rows are empty: giving up
No such file or directory at /cm/shared/apps/wgddetector/1.1/WGDdetector-1.1/bin/sub_ks_family.pl line 10.
Could you please help me to resolve these errors?
Thanks in advance.
Regards, Jithin
