Closed sklasek closed 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
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-- Liat Shenhav
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
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.
-- Liat Shenhav
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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
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.
-- Liat Shenhav
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-- Liat Shenhav
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 <
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.
-- Liat Shenhav
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.
-- Liat Shenhav
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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
Hmm, that's what I've been doing. I'm responding on github directly, let me know if this works. My apologies.
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 <
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.
-- Liat Shenhav
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-- Liat Shenhav
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-- Liat Shenhav
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Dear Scott,
I was able to run FEAST with the data files you sent me. A few important comments:
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")
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 <
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.
-- Liat Shenhav
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-- Liat Shenhav
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-- Liat Shenhav
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-- Liat Shenhav
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
Hi Sott, I have the same problem, what was the misake in your case ? I am stocked here Thank you Zeina
Hi, @sklasek and @sklasek I am still facing this same error. What was the misunderstanding that fixed it? @sklasek
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
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.
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:
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