New problems in generating Manhattan plot

[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

[alachins]

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 — Reply to this email directly, view it on GitHub <#53>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCU2FSPXPZESODYVDD3ZK2ERXAVCNFSM6AAAAABKNC3JWSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TENBYG43TSNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[yixuanyang27]

Dear Nikos, Sorry for the late reply and thank you for your reply. You can find my test.vcf in the attachment. The version I use is version 2.9. Thank you for your time. Best regards, Yixuan test.vcf <https://drive.google.com/file/d/13zXsvTbsI-4DePyI7PxEz1iVJ486kt9W/view?usp=drive_web>

…

On Fri, Jul 12, 2024 at 3:17 PM alachins ***@***.***> wrote: 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 > > — > Reply to this email directly, view it on GitHub > <#53>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AALKWCU2FSPXPZESODYVDD3ZK2ERXAVCNFSM6AAAAABKNC3JWSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TENBYG43TSNI> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- Nikolaos Alachiotis — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BHWWHFJMXOKPP7465KMXSOLZL7JM7AVCNFSM6AAAAABKNC3JWSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRVGU3TCNZXGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>