Incomplete MAPS output

[aperreault]

Hi again!

I've gotten my data mostly through the MAPS pipeline but the final step cannot be completed. The output in terminal shows that the regression is run on all chromosomes and there is output in the MAPS_output directory. This is the final part of the output in terminal: [1] "finding peaks" [1] 12 31 Error in seq.default(1, length(y), 1) : wrong sign in 'by' argument Calls: classify_peaks -> cbind -> seq -> seq.default Execution halted Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'output_v5/MAPS_output/filename_20190411_092821/filename.5k.2.peaks': No such file or directory Execution halted third

Any advice on what's going wrong here? Thanks! -Andrea

[zhuyezhang]

I have met similar problems and I have no idea how to solve it. Could anyone give me some advice? Thanks very much in advance!

Yezhang

[ijuric]

Hi Yezhang, Sorry about the issue. As more people use it, we're learning that MAPS is not good at telling what went wrong, and we're working on adding additional messaging when something goes wrong. It seems that MAPS is not finding any significant 3D interactions at this resolution. Did you try running MAPS at 10kb resolution? Btw. how many reads do you have ? There should be bunch of .MAPS2_pospoisson files in MAPS_output directory. Open them in R and check how many rows you have with number in "count" column 12 or more, it should give you a rough estimate about the upper limit on the number of significant 3D interactions. 12 is a hard cutoff, so if you don't have many (or any) bin pairs with 12 or more reads, you won't find any interactions.

Hope it helps, Ivan

On Mon, May 6, 2019 at 6:14 AM zhuyezhang notifications@github.com wrote:

I have met similar problems and I have no idea how to solve it. Could anyone give me some advice? Thanks very much in advance!

Yezhang

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ijuric/MAPS/issues/7#issuecomment-489571753, or mute the thread https://github.com/notifications/unsubscribe-auth/ACZ6SZNUAKHFFSZA53S6JOLPUAAHDANCNFSM4HFQS3KA .

[ijuric]

I've added an error msg. Now, if you run MAPS but there are no bin pairs which can be significant interactions, MAPS will crash with an error message telling you what the problem is.

On Mon, May 6, 2019 at 9:38 AM Ivan Juric ivan.juric.gen@gmail.com wrote:

Hi Yezhang, Sorry about the issue. As more people use it, we're learning that MAPS is not good at telling what went wrong, and we're working on adding additional messaging when something goes wrong. It seems that MAPS is not finding any significant 3D interactions at this resolution. Did you try running MAPS at 10kb resolution? Btw. how many reads do you have ? There should be bunch of .MAPS2_pospoisson files in MAPS_output directory. Open them in R and check how many rows you have with number in "count" column 12 or more, it should give you a rough estimate about the upper limit on the number of significant 3D interactions. 12 is a hard cutoff, so if you don't have many (or any) bin pairs with 12 or more reads, you won't find any interactions.

Hope it helps, Ivan

On Mon, May 6, 2019 at 6:14 AM zhuyezhang notifications@github.com wrote:

I have met similar problems and I have no idea how to solve it. Could anyone give me some advice? Thanks very much in advance!

Yezhang

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ijuric/MAPS/issues/7#issuecomment-489571753, or mute the thread https://github.com/notifications/unsubscribe-auth/ACZ6SZNUAKHFFSZA53S6JOLPUAAHDANCNFSM4HFQS3KA .

[zhuyezhang]

Hi Ivan,

Thanks a million for your kind help.

Indeed, I have tried running MAPS at 10kb resolution and got a few (~40) interactions which are too little for this sample. I have about 100 million reads for this PLAC-Seq sample. Perhaps, there was something wrong when preparing the library.

Thanks again for your help. I will do some troubleshooting later and I may have to bother you again.

Best, Yezhang

原始邮件 发件人:ijuricnotifications@github.com 收件人:ijuric/MAPSMAPS@noreply.github.com 抄送:zhuyezhang11707072@zju.edu.cn; Commentcomment@noreply.github.com 发送时间:2019年5月6日(周一) 22:11 主题:Re: [ijuric/MAPS] Incomplete MAPS output (#7)

I've added an error msg. Now, if you run MAPS but there are no bin pairs which can be significant interactions, MAPS will crash with an error message telling you what the problem is.

On Mon, May 6, 2019 at 9:38 AM Ivan Juric ivan.juric.gen@gmail.com wrote:

Hi Yezhang, Sorry about the issue. As more people use it, we're learning that MAPS is not good at telling what went wrong, and we're working on adding additional messaging when something goes wrong. It seems that MAPS is not finding any significant 3D interactions at this resolution. Did you try running MAPS at 10kb resolution? Btw. how many reads do you have ? There should be bunch of .MAPS2_pospoisson files in MAPS_output directory. Open them in R and check how many rows you have with number in "count" column 12 or more, it should give you a rough estimate about the upper limit on the number of significant 3D interactions. 12 is a hard cutoff, so if you don't have many (or any) bin pairs with 12 or more reads, you won't find any interactions.

Hope it helps, Ivan

On Mon, May 6, 2019 at 6:14 AM zhuyezhang notifications@github.com wrote:

I have met similar problems and I have no idea how to solve it. Could anyone give me some advice? Thanks very much in advance!

Yezhang

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub ,">https://github.com/ijuric/MAPS/issues/7#issuecomment-489571753, or mute the thread ">https://github.com/notifications/unsubscribe-auth/ACZ6SZNUAKHFFSZA53S6JOLPUAAHDANCNFSM4HFQS3KA .

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