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Fast expectation maximization for microbial source tracking
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error running FEAST: Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed #15

Closed sklasek closed 4 years ago

sklasek commented 4 years ago

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below: 

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo")
Error in if (sum(x[i, ]) > maxdepth) { :  missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

liashenhav commented 4 years ago

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek notifications@github.com wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA .

-- Liat Shenhav

sklasek commented 4 years ago

Hi Liat,

Unfortunately, the rownames of the two files are identical. I've attached the files below for your reference.

Thank you, Scott

On Wed, Jun 17, 2020 at 4:45 PM liashenhav notifications@github.com wrote:

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek notifications@github.com wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15#issuecomment-645614949, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANDH7ZRI2DHCR3PLH3PW5KDRXETNXANCNFSM4OA6BFHA .

liashenhav commented 4 years ago

Attachment?

On Wed, Jun 17, 2020 at 7:25 PM Scott Klasek notifications@github.com wrote:

Hi Liat,

Unfortunately, the rownames of the two files are identical. I've attached the files below for your reference.

Thank you, Scott

On Wed, Jun 17, 2020 at 4:45 PM liashenhav notifications@github.com wrote:

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek notifications@github.com wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15#issuecomment-645614949, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ANDH7ZRI2DHCR3PLH3PW5KDRXETNXANCNFSM4OA6BFHA

.

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-- Liat Shenhav

sklasek commented 4 years ago

Hi Liat, Sorry, looks like I only replied to you. Files are attached here. Best, Scott

On Thu, Jun 18, 2020 at 1:22 AM liashenhav notifications@github.com wrote:

Attachment?

On Wed, Jun 17, 2020 at 7:25 PM Scott Klasek notifications@github.com wrote:

Hi Liat,

Unfortunately, the rownames of the two files are identical. I've attached the files below for your reference.

Thank you, Scott

On Wed, Jun 17, 2020 at 4:45 PM liashenhav notifications@github.com wrote:

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek <notifications@github.com

wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15#issuecomment-645614949, or unsubscribe <

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.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15#issuecomment-645730285, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AIQ7SAXMFF5XRLB4GL4AOCLRXF3JJANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15#issuecomment-645780545, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANDH7ZRYDOJF6XYZN2NJXFLRXGQBLANCNFSM4OA6BFHA .

liashenhav commented 4 years ago

Sorry Scott, still no files. Probably best to send it directly from your email address.

On Fri, Jun 19, 2020 at 8:15 AM Scott Klasek notifications@github.com wrote:

Hi Liat, Sorry, looks like I only replied to you. Files are attached here. Best, Scott

On Thu, Jun 18, 2020 at 1:22 AM liashenhav notifications@github.com wrote:

Attachment?

On Wed, Jun 17, 2020 at 7:25 PM Scott Klasek notifications@github.com wrote:

Hi Liat,

Unfortunately, the rownames of the two files are identical. I've attached the files below for your reference.

Thank you, Scott

On Wed, Jun 17, 2020 at 4:45 PM liashenhav notifications@github.com wrote:

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek < notifications@github.com

wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/cozygene/FEAST/issues/15#issuecomment-645614949 , or unsubscribe <

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.

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.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15#issuecomment-645780545, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ANDH7ZRYDOJF6XYZN2NJXFLRXGQBLANCNFSM4OA6BFHA

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— You are receiving this because you commented.

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-- Liat Shenhav

sklasek commented 4 years ago

Hmm, that's what I've been doing. I'm responding on github directly, let me know if this works. My apologies.

feasttest.zip

sklasek commented 4 years ago

Hi Liat, Just wondering whether you received my files and were able to reproduce my error. I had been attaching them as .csvs and sending them via email, later to learn github does not accept .csv file uploads. Thanks, Scott

On Fri, Jun 19, 2020 at 12:16 PM liashenhav notifications@github.com wrote:

Sorry Scott, still no files. Probably best to send it directly from your email address.

On Fri, Jun 19, 2020 at 8:15 AM Scott Klasek notifications@github.com wrote:

Hi Liat, Sorry, looks like I only replied to you. Files are attached here. Best, Scott

On Thu, Jun 18, 2020 at 1:22 AM liashenhav notifications@github.com wrote:

Attachment?

On Wed, Jun 17, 2020 at 7:25 PM Scott Klasek <notifications@github.com

wrote:

Hi Liat,

Unfortunately, the rownames of the two files are identical. I've attached the files below for your reference.

Thank you, Scott

On Wed, Jun 17, 2020 at 4:45 PM liashenhav <notifications@github.com

wrote:

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek < notifications@github.com

wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/cozygene/FEAST/issues/15#issuecomment-645614949 , or unsubscribe <

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.

-- Liat Shenhav

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-- Liat Shenhav

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liashenhav commented 4 years ago

Dear Scott,

I was able to run FEAST with the data files you sent me. A few important comments:

  1. You got an error message since your count matrix is saved in transpose. FEAST is expecting the taxa in the rows and the samples in the columns. A simple solution is using t(otus) after reading the OTU file using the function 'Load_CountMatrix'.

Specifically:

otus <- Load_CountMatrix(CountMatrix_path = "~/Downloads/feasttest/myotutable.txt") FEAST_output <- FEAST(C = t(otus), metadata = metadata, different_sources_flag = 1, dir_path = "~/FEAST/Data_files/", outfile="demo")

  1. In your metadata file, I see that multiple sinks get the same Id (which will throw an error). To properly address that I've created a separate branch called 'Nonunique_sources'. See the attached code + data that converts the metadata to allow repeated sources + allowS repeated sources in FEAST. This code should allow you to run FEAST from end-to-end on your data (just make sure to change the directory paths whenever indicated).

Let me know if that works.

Thanks,

Liat

On Tue, Jun 23, 2020 at 7:57 AM Scott Klasek notifications@github.com wrote:

Hi Liat, Just wondering whether you received my files and were able to reproduce my error. I had been attaching them as .csvs and sending them via email, later to learn github does not accept .csv file uploads. Thanks, Scott

On Fri, Jun 19, 2020 at 12:16 PM liashenhav notifications@github.com wrote:

Sorry Scott, still no files. Probably best to send it directly from your email address.

On Fri, Jun 19, 2020 at 8:15 AM Scott Klasek notifications@github.com wrote:

Hi Liat, Sorry, looks like I only replied to you. Files are attached here. Best, Scott

On Thu, Jun 18, 2020 at 1:22 AM liashenhav notifications@github.com wrote:

Attachment?

On Wed, Jun 17, 2020 at 7:25 PM Scott Klasek < notifications@github.com

wrote:

Hi Liat,

Unfortunately, the rownames of the two files are identical. I've attached the files below for your reference.

Thank you, Scott

On Wed, Jun 17, 2020 at 4:45 PM liashenhav < notifications@github.com

wrote:

Hi Scott,

It usually happens when the row names in the metadata and otu table don’t match. Can you please check that first? If this doesn’t help, please share the metadata + data files. I’ll try to reproduce this error and debug it for you.

Thanks,

Liat

On Wed, Jun 17, 2020 at 1:24 PM Scott Klasek < notifications@github.com

wrote:

Hello,

I am trying to run FEAST on a 16S dataset of 89 samples and have encountered an error while running the algorithm. Command and error below:

feast.block <- FEAST(C = myotutable, metadata = f.block.metadata, different_sources_flag = 1, dir_path = ".", outfile="demo") Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed

This seems to imply that I've got NA values in my metadata or otu table, but I checked and I don't. I also wasn't aware any input from the metadata table takes TRUE/FALSE values, am I mistaken? Just to double check, I verified that changing other parameters (different_sources_flag, COVERAGE) didn't prevent this error from occurring.

I was able to load the input files and run the FEAST demo from the github repo just fine.

Versions I'm running: R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) FEAST_0.1.0

Thanks, Scott

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cozygene/FEAST/issues/15, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AIQ7SAVD7JBTOM7734IIAOLRXEQ7PANCNFSM4OA6BFHA

.

-- Liat Shenhav

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/cozygene/FEAST/issues/15#issuecomment-645614949 , or unsubscribe <

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-- Liat Shenhav

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-- Liat Shenhav

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-- Liat Shenhav

sklasek commented 4 years ago

Hi Liat, Thanks for the reply– I misunderstood how the IDs work. I subset my dataframe by the treatments I was interested in, assigned sink communities unique IDs, source communities NAs, and was able to run FEAST successfully. I didn't need to transpose my OTU table– in fact, trying with samples as columns threw another error: Error in sprintf("Error: there are %d sample ids in common ") : too few arguments). Anyway, I think the original error came about because of my misunderstanding, so I'll close the issue. Thanks for looking into this! Scott

zina-R commented 2 years ago

Hi Sott, I have the same problem, what was the misake in your case ? I am stocked here Thank you Zeina

yangchen2 commented 6 months ago

Hi, @sklasek and @sklasek I am still facing this same error. What was the misunderstanding that fixed it? @sklasek

jyotsnepal commented 1 month ago

Hi could you please share the metadata format in case of multiple similar source and sinks. Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In matrix(sinks, nrow = 1, ncol = dim(totalsource)[2]) : data length differs from size of matrix: [54546 != 1 x 9091] 2: In matrix(sinks, nrow = 1, ncol = dim(totalsource)[2]) : data length differs from size of matrix: [1345468 != 1 x 9091] 3: In matrix(sinks, nrow = 1, ncol = dim(totalsource)[2]) : data length differs from size of matrix: [1390923 != 1 x 9091]

I keep getting this type of error and I do not understand why

makochann commented 1 week ago

Hi could you please share the metadata format in case of multiple similar source and sinks. Error in if (sum(x[i, ]) > maxdepth) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In matrix(sinks, nrow = 1, ncol = dim(totalsource)[2]) : data length differs from size of matrix: [54546 != 1 x 9091] 2: In matrix(sinks, nrow = 1, ncol = dim(totalsource)[2]) : data length differs from size of matrix: [1345468 != 1 x 9091] 3: In matrix(sinks, nrow = 1, ncol = dim(totalsource)[2]) : data length differs from size of matrix: [1390923 != 1 x 9091]

I keep getting this type of error and I do not understand why

Due to my source group having multiple samples, I tried setting different IDs for each sample, such as 1, 2, 3... In the end, this error was resolved. I was wondering if it could help you.