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KO table all zero #15

Open emilceviruel opened 3 years ago

emilceviruel commented 3 years ago

Hi. I've tried to make functional prediction but KO table is all zeros. I can't find the mistake. Can anybody help me?

gailrosen commented 3 years ago

Dear Emilce,

Thank you for your interest in the package. Do you have the code that you tried to run and example input so that we can try to reproduce the bug? When we get this info, I will defer to Steve to answer your question.

thank you and best, Gail

From: emilceviruel notifications@github.com Sent: Monday, January 4, 2021 1:48 PM To: EESI/themetagenomics Cc: Subscribed Subject: [EESI/themetagenomics] KO table all zero (#15)

External.

Hi. I've tried to make functional prediction but KO table is all zeros. I can't find the mistake. Can anybody help me?

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emilceviruel commented 3 years ago

Dear Gail.

Thank you for your reply

I ran exactly the code in http://127.0.0.1:25564/library/themetagenomics/doc/thematic_structure.R, using the Rdata attached. I tried with your data (DAVID) and it worked. But with my data KO is all in zeros. It worked with my data stil KO table. That step didn´t work. I lost that R code accidentally, and I tried to run again with the same Rdata, but I get this message:

CLEAN <- prepare_data(otu_table=OTU,+ rows_are_taxa=FALSE,+ tax_table=TAX,+ metadata=META,+ formula=~pH + Nt + SOC + EC,+ cn_normalize=FALSE,+ drop=TRUE)> system.time(TOPICS <- find_topics(CLEAN,K=15)) user system elapsed 15.80 2.87 18.81 > TOPICSA topics object containing a topic model with 15 topics, 12 samples and 4654 discrete taxa.> TOPIC_EFFECTSError: objeto 'TOPIC_EFFECTS' no encontrado (object not found)

tmp <- tempdir()> download_ref(tmp,reference='gg_ko',overwrite=FALSE)> system.time(FUNCTIONS <- picrust(OTU,rows_are_taxa=FALSE,+ reference='gg_ko',reference_path=tmp,+ cn_normalize=TRUE,sample_normalize=FALSE,+ drop=TRUE))Error in copy_numbers[otus_to_load, ] : subíndice fuera de los límites ( sub-index out of limits) Timing stopped at: 0.58 0 0.71

I'll be very grateful if you help me to do this analysis, because this data will be published soon.

Thank you best regards

Emilce

El lun, 4 ene 2021 a las 22:49, gailrosen (notifications@github.com) escribió:

Dear Emilce,

Thank you for your interest in the package. Do you have the code that you tried to run and example input so that we can try to reproduce the bug? When we get this info, I will defer to Steve to answer your question.

thank you and best, Gail

From: emilceviruel notifications@github.com Sent: Monday, January 4, 2021 1:48 PM To: EESI/themetagenomics Cc: Subscribed Subject: [EESI/themetagenomics] KO table all zero (#15)

External.

Hi. I've tried to make functional prediction but KO table is all zeros. I can't find the mistake. Can anybody help me?

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gailrosen commented 3 years ago

Thanks. Can you give an excerpt of the Rdata file that you are working with? Because otherwise, Steve will don't know why it's not annotating the KOs of it.

Like could you show snippets of your tables that you're feeding the program?

From: emilceviruel notifications@github.com Sent: Wednesday, January 6, 2021 8:38 AM To: EESI/themetagenomics Cc: Rosen,Gail; Comment Subject: Re: [EESI/themetagenomics] KO table all zero (#15)

External.

Dear Gail.

Thank you for your reply

I ran exactly the code in http://127.0.0.1:25564/library/themetagenomics/doc/thematic_structure.R, using the Rdata attached. I tried with your data (DAVID) and it worked. But with my data KO is all in zeros. It worked with my data stil KO table. That step didn´t work. I lost that R code accidentally, and I tried to run again with the same Rdata, but I get this message:

CLEAN <- prepare_data(otu_table=OTU,+ rows_are_taxa=FALSE,+ tax_table=TAX,+ metadata=META,+ formula=~pH + Nt + SOC + EC,+ cn_normalize=FALSE,+ drop=TRUE)> system.time(TOPICS <- find_topics(CLEAN,K=15)) user system elapsed 15.80 2.87 18.81 > TOPICSA topics object containing a topic model with 15 topics, 12 samples and 4654 discrete taxa.> TOPIC_EFFECTSError: objeto 'TOPIC_EFFECTS' no encontrado (object not found)

tmp <- tempdir()> download_ref(tmp,reference='gg_ko',overwrite=FALSE)> system.time(FUNCTIONS <- picrust(OTU,rows_are_taxa=FALSE,+ reference='gg_ko',reference_path=tmp,+ cn_normalize=TRUE,sample_normalize=FALSE,+ drop=TRUE))Error in copy_numbers[otus_to_load, ] : subíndice fuera de los límites ( sub-index out of limits) Timing stopped at: 0.58 0 0.71

I'll be very grateful if you help me to do this analysis, because this data will be published soon.

Thank you best regards

Emilce

El lun, 4 ene 2021 a las 22:49, gailrosen (notifications@github.com) escribió:

Dear Emilce,

Thank you for your interest in the package. Do you have the code that you tried to run and example input so that we can try to reproduce the bug? When we get this info, I will defer to Steve to answer your question.

thank you and best, Gail

From: emilceviruel notifications@github.com Sent: Monday, January 4, 2021 1:48 PM To: EESI/themetagenomics Cc: Subscribed Subject: [EESI/themetagenomics] KO table all zero (#15)

External.

Hi. I've tried to make functional prediction but KO table is all zeros. I can't find the mistake. Can anybody help me?

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emilceviruel commented 3 years ago

Thanks Gail,

What did you mean with "excerpt of the Rdata file"? Do you need the .txt files?

Snippets of my tables

OTU [1:5,1:5] 0001 0002 0003 0004 0005 ZT1 2183 478 155 195 342 ZT2 1973 438 130 146 291 ZT3 1973 488 137 150 274 CT1 1690 696 137 124 533 CT2 2070 787 146 157 529

TAX [1:5,1:5] Phylum Class Order 0001 "Firmicutes" "Bacilli" "Bacillales" 0002 "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" 0003 "Firmicutes" "Bacilli" "Bacillales" 0004 "Firmicutes" "Bacilli" "Bacillales" 0005 "Firmicutes" "Bacilli" "Bacillales" Family Genus 0001 "Bacillaceae" "Bacillus" 0002 "Sphingomonadaceae" "Kaistobacter" 0003 "Planococcaceae" "Sporosarcina" 0004 "Planococcaceae" "Lysinibacillus" 0005 "Bacillaceae" "Bacillus"

pH Nt SOC EC ZT1 6.14 0.1503026 3.372611 1.14 ZT2 5.97 0.1528803 3.251034 0.95 ZT3 6.03 0.1626240 3.487586 0.98 CT1 6.60 0.1269904 3.219310 1.60

Emilce

El mié, 6 ene 2021 a las 12:49, gailrosen (notifications@github.com) escribió:

Thanks. Can you give an that you are working with? Because otherwise, Steve will don't know why it's not annotating the KOs of it.

Like could you show snippets of your tables that you're feeding the program?

From: emilceviruel notifications@github.com Sent: Wednesday, January 6, 2021 8:38 AM To: EESI/themetagenomics Cc: Rosen,Gail; Comment Subject: Re: [EESI/themetagenomics] KO table all zero (#15)

External.

Dear Gail.

Thank you for your reply

I ran exactly the code in http://127.0.0.1:25564/library/themetagenomics/doc/thematic_structure.R, using the Rdata attached. I tried with your data (DAVID) and it worked. But with my data KO is all in zeros. It worked with my data stil KO table. That step didn´t work. I lost that R code accidentally, and I tried to run again with the same Rdata, but I get this message:

CLEAN <- prepare_data(otu_table=OTU,+ rows_are_taxa=FALSE,+ tax_table=TAX,+ metadata=META,+ formula=~pH + Nt + SOC + EC,+ cn_normalize=FALSE,+ drop=TRUE)> system.time(TOPICS <- find_topics(CLEAN,K=15)) user system elapsed 15.80 2.87 18.81 > TOPICSA topics object containing a topic model with 15 topics, 12 samples and 4654 discrete taxa.> TOPIC_EFFECTSError: objeto 'TOPIC_EFFECTS' no encontrado (object not found)

tmp <- tempdir()> download_ref(tmp,reference='gg_ko',overwrite=FALSE)> system.time(FUNCTIONS <- picrust(OTU,rows_are_taxa=FALSE,+ reference='gg_ko',reference_path=tmp,+ cn_normalize=TRUE,sample_normalize=FALSE,+ drop=TRUE))Error in copy_numbers[otus_to_load, ] : subíndice fuera de los límites ( sub-index out of limits) Timing stopped at: 0.58 0 0.71

I'll be very grateful if you help me to do this analysis, because this data will be published soon.

Thank you best regards

Emilce

El lun, 4 ene 2021 a las 22:49, gailrosen (notifications@github.com) escribió:

Dear Emilce,

Thank you for your interest in the package. Do you have the code that you tried to run and example input so that we can try to reproduce the bug? When we get this info, I will defer to Steve to answer your question.

thank you and best, Gail

From: emilceviruel notifications@github.com Sent: Monday, January 4, 2021 1:48 PM To: EESI/themetagenomics Cc: Subscribed Subject: [EESI/themetagenomics] KO table all zero (#15)

External.

Hi. I've tried to make functional prediction but KO table is all zeros. I can't find the mistake. Can anybody help me?

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emilceviruel commented 3 years ago

Hi Gail

I just found the mistake. It was a wrong bacteria's name in the taxonomy table. So, I got the KO table.

Thanks for your attention anyway.

Best

Emilce

El mié., 6 de enero de 2021 2:09 p. m., Emilce Viruel emiviruel@gmail.com escribió:

Thanks Gail,

What did you mean with "excerpt of the Rdata file"? Do you need the .txt files?

Snippets of my tables

OTU [1:5,1:5] 0001 0002 0003 0004 0005 ZT1 2183 478 155 195 342 ZT2 1973 438 130 146 291 ZT3 1973 488 137 150 274 CT1 1690 696 137 124 533 CT2 2070 787 146 157 529

TAX [1:5,1:5] Phylum Class Order 0001 "Firmicutes" "Bacilli" "Bacillales" 0002 "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" 0003 "Firmicutes" "Bacilli" "Bacillales" 0004 "Firmicutes" "Bacilli" "Bacillales" 0005 "Firmicutes" "Bacilli" "Bacillales" Family Genus 0001 "Bacillaceae" "Bacillus" 0002 "Sphingomonadaceae" "Kaistobacter" 0003 "Planococcaceae" "Sporosarcina" 0004 "Planococcaceae" "Lysinibacillus" 0005 "Bacillaceae" "Bacillus"

pH Nt SOC EC ZT1 6.14 0.1503026 3.372611 1.14 ZT2 5.97 0.1528803 3.251034 0.95 ZT3 6.03 0.1626240 3.487586 0.98 CT1 6.60 0.1269904 3.219310 1.60

Emilce

El mié, 6 ene 2021 a las 12:49, gailrosen (notifications@github.com) escribió:

Thanks. Can you give an that you are working with? Because otherwise, Steve will don't know why it's not annotating the KOs of it.

Like could you show snippets of your tables that you're feeding the program?

From: emilceviruel notifications@github.com Sent: Wednesday, January 6, 2021 8:38 AM To: EESI/themetagenomics Cc: Rosen,Gail; Comment Subject: Re: [EESI/themetagenomics] KO table all zero (#15)

External.

Dear Gail.

Thank you for your reply

I ran exactly the code in http://127.0.0.1:25564/library/themetagenomics/doc/thematic_structure.R, using the Rdata attached. I tried with your data (DAVID) and it worked. But with my data KO is all in zeros. It worked with my data stil KO table. That step didn´t work. I lost that R code accidentally, and I tried to run again with the same Rdata, but I get this message:

CLEAN <- prepare_data(otu_table=OTU,+ rows_are_taxa=FALSE,+ tax_table=TAX,+ metadata=META,+ formula=~pH + Nt + SOC + EC,+ cn_normalize=FALSE,+ drop=TRUE)> system.time(TOPICS <- find_topics(CLEAN,K=15)) user system elapsed 15.80 2.87 18.81 > TOPICSA topics object containing a topic model with 15 topics, 12 samples and 4654 discrete taxa.> TOPIC_EFFECTSError: objeto 'TOPIC_EFFECTS' no encontrado (object not found)

tmp <- tempdir()> download_ref(tmp,reference='gg_ko',overwrite=FALSE)> system.time(FUNCTIONS <- picrust(OTU,rows_are_taxa=FALSE,+ reference='gg_ko',reference_path=tmp,+ cn_normalize=TRUE,sample_normalize=FALSE,+ drop=TRUE))Error in copy_numbers[otus_to_load, ] : subíndice fuera de los límites ( sub-index out of limits) Timing stopped at: 0.58 0 0.71

I'll be very grateful if you help me to do this analysis, because this data will be published soon.

Thank you best regards

Emilce

El lun, 4 ene 2021 a las 22:49, gailrosen (notifications@github.com) escribió:

Dear Emilce,

Thank you for your interest in the package. Do you have the code that you tried to run and example input so that we can try to reproduce the bug? When we get this info, I will defer to Steve to answer your question.

thank you and best, Gail

From: emilceviruel notifications@github.com Sent: Monday, January 4, 2021 1:48 PM To: EESI/themetagenomics Cc: Subscribed Subject: [EESI/themetagenomics] KO table all zero (#15)

External.

Hi. I've tried to make functional prediction but KO table is all zeros. I can't find the mistake. Can anybody help me?

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