alachins
commented
1 month ago Hi Yixuan,
Can you please send me the test.vcf to take a look? Which version are you using?
Best regards, Nikos A.
On Fri, Jul 5, 2024 at 2:12 PM yixuanyang27 @.***> wrote:
Hello Nikolaos and Pavlos, I understand there were issues about Mahattan plots already asked by other ppl. However, I am encoutering something new that others did not mention. I am hoping to get some help here.
My input vcf contains information of a fungus with 10 chromosomes+mitochondrial_genome. I used the command "./RAiSD -n vcf_test -I ~/RAiSD/data/test.vcf -f -A 0.995" to generate a Manhattan plot. I was able to obtain RAiSD_Info.vcf_test, a full RAiSD_Report.vcf_test, and RAiSD_Report.vcf_test for each chromosome. The Mahattan plot generated unfortunately was empty named "RAiSD_ManhattanPlot.NA.pdf". By inspecting the reports generated separetely by each chromosome, I noticed the empty RAiSD_Report.vcf_test.mitochondrial_genome might be the cause of the issue. In addition my full report RAiSD_Report.vcf_test only contains two columns, not sure if it is also a problem.
gwdu102:75 14:08:18 ~/RAiSD/raisd-master > head RAiSD_Report.vcf_test // chr1 21000 6.283e-11 22276 5.980e-11 23316 5.727e-11 23889 5.868e-11 24193 7.807e-11 24693 7.648e-11 25606 7.445e-11 26160 7.413e-11 26455 7.168e-11
I downloaded your Rscript for generating the Manhattan plot. I ran the Rscript after deleting the RAiSD_Report.vcf_test.mitochondrial_genome file. However, there was an error "Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'RAiSD_ReportList.NA.txt': No such file or directory Execution halted".
In addition, ./RAiSD -n ms_test -I ~/RAiSD/data/ms.out -L 100000 -A 0.995 -f for the test data works perfectly fine.
Look forward to hearding back from you soon.
Cheers,
Yixuan
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-- Nikolaos Alachiotis
yixuanyang27
Hello Nikolaos and Pavlos, I understand there were issues about Mahattan plots already asked by other ppl. However, I am encoutering something new that others did not mention. I am hoping to get some help here.
My input vcf contains information of a fungus with 10 chromosomes+mitochondrial_genome. I used the command "./RAiSD -n vcf_test -I ~/RAiSD/data/test.vcf -f -A 0.995" to generate a Manhattan plot. I was able to obtain RAiSD_Info.vcf_test, a full RAiSD_Report.vcf_test, and RAiSD_Report.vcf_test for each chromosome. The Mahattan plot generated unfortunately was empty named "RAiSD_ManhattanPlot.NA.pdf". By inspecting the reports generated separetely by each chromosome, I noticed the empty RAiSD_Report.vcf_test.mitochondrial_genome might be the cause of the issue. (Also no scores for Set mitochondrial_genome). In addition my full report RAiSD_Report.vcf_test only contains two columns, not sure if it is also a problem.
gwdu102:75 14:08:18 ~/RAiSD/raisd-master > head RAiSD_Report.vcf_test // chr1 21000 6.283e-11 22276 5.980e-11 23316 5.727e-11 23889 5.868e-11 24193 7.807e-11 24693 7.648e-11 25606 7.445e-11 26160 7.413e-11 26455 7.168e-11
In addition, ./RAiSD -n ms_test -I ~/RAiSD/data/ms.out -L 100000 -A 0.995 -f for the test data works perfectly fine.
Look forward to hearding back from you soon.
Cheers,
Yixuan