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reimandlab / ActiveDriverWGSR

ActiveDriverWGSR is an R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data
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Error in glm.fit: object fit not found #17

Open skanwal opened 8 months ago

skanwal commented 8 months ago

Hi @reimand0 ,

I am getting an error, when trying to run ActiveDriveWGS using following command:

ActiveDriverWGS.res[[i]] = ActiveDriverWGS(mutations = ActiveDriverWGSInfo[[i]], elements = elements, sites = NULL, window_size = 50000, recovery.dir = paste(outDir, "ActiveDriverWGS_recovery", sep="/"), mc.cores = 4, ref_genome = paste0("hg", params$ucsc_genome_assembly))

The error is:

0 remove hypermut, n= 0 ,  0 %
hypermuted samples:   

reversing 0 positions
Removing  0  invalid SNVs & indels

Number of Elements with 0 Mutations:  14 
Tests to do:  1195 
Tests recovered:  928 
100  elements completed
200  elements completed
300  elements completed
400  elements completed
500  elements completed
600  elements completed
700  elements completed
800  elements completed
900  elements completed
.Error in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL,  : 
  object 'fit' not found

Data

>  head(ActiveDriverWGSInfo)
$pdac
         chr      pos1      pos2 ref alt                            patient
     1: chr3 120002137 120002137   T   C p010_tumor-52fccd-somatic.pcgr.vcf
     2: chr4 125450687 125450687   G   T p010_tumor-52fccd-somatic.pcgr.vcf
     3: chr5  38502681  38502681   C   A p010_tumor-52fccd-somatic.pcgr.vcf
     4: chr6  89951675  89951675   C   T p010_tumor-52fccd-somatic.pcgr.vcf
     5: chr7  82822603  82822603   G   T p010_tumor-52fccd-somatic.pcgr.vcf
    ---                                                                    
196698: chrX  15795073  15795073   A   C                  SA533811_SP125786
196699: chrX  15800132  15800132   T   A                  SA569276_SP133702
196700: chrX  15803607  15803607   G   T                  SA558660_SP125807
196701: chr9  14398633  14398633   C   G                            CGPA229
196702: chr1 186680291 186680291   C   T                            CGPA234

> str(ActiveDriverWGSInfo)
List of 1
 $ pdac:Classes 'data.table' and 'data.frame':  196702 obs. of  6 variables:
  ..$ chr    : chr [1:196702] "chr3" "chr4" "chr5" "chr6" ...
  ..$ pos1   : num [1:196702] 1.20e+08 1.25e+08 3.85e+07 9.00e+07 8.28e+07 ...
  ..$ pos2   : num [1:196702] 1.20e+08 1.25e+08 3.85e+07 9.00e+07 8.28e+07 ...
  ..$ ref    : chr [1:196702] "T" "G" "C" "C" ...
  ..$ alt    : chr [1:196702] "C" "T" "A" "T" ...
  ..$ patient: chr [1:196702] "p010_tumor-52fccd-somatic.pcgr.vcf" "p010_tumor-52fccd-somatic.pcgr.vcf" "p010_tumor-52fccd-somatic.pcgr.vcf" "p010_tumor-52fccd-somatic.pcgr.vcf" ...
  ..- attr(*, ".internal.selfref")=<externalptr>

  > head(elements)
     chr    start      end       id          GENEID
20 chr12   912077   990053    RAD52 ENSG00000002016
30 chr17 38869859 38921770    LASP1 ENSG00000002834
56 chr12 21468911 21501669    RECQL ENSG00000004700
66  chr7 96120220 96322147 SLC25A13 ENSG00000004864
74 chr19 18831938 18868236     UPF1 ENSG00000005007
78  chr7 27181510 27185223   HOXA11 ENSG00000005073

I have also done some sanity checking on both mutation and elements data and found no issues with having NA's or empty values.

Can you please help figure out why this might be producing an error? Many thanks.

reimand0 commented 8 months ago

Thanks for the message. Can you please share a reproducible example? If you are comfortable sharing the dataset you can email it to me @.***

Best, Jüri

On Tue, Mar 5, 2024 at 18:54 Sehrish Kanwal @.***> wrote:

Hi @reimand0 https://github.com/reimand0 ,

I am getting an error, when trying to run ActiveDriveWGS using following command:

ActiveDriverWGS.res[[i]] = ActiveDriverWGS(mutations = ActiveDriverWGSInfo[[i]], elements = elements, sites = NULL, window_size = 50000, recovery.dir = paste(outDir, "ActiveDriverWGS_recovery", sep="/"), mc.cores = params$activedriverwgs_cores, ref_genome = paste0("hg", params$ucsc_genome_assembly))

The error is:

0 remove hypermut, n= 0 , 0 % hypermuted samples:

reversing 0 positions Removing 0 invalid SNVs & indels

Number of Elements with 0 Mutations: 14 Tests to do: 1195 Tests recovered: 928 100 elements completed 200 elements completed 300 elements completed 400 elements completed 500 elements completed 600 elements completed 700 elements completed 800 elements completed 900 elements completed .Error in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL, : object 'fit' not found

Data

head(ActiveDriverWGSInfo) $pdac chr pos1 pos2 ref alt patient 1: chr3 120002137 120002137 T C p010_tumor-52fccd-somatic.pcgr.vcf 2: chr4 125450687 125450687 G T p010_tumor-52fccd-somatic.pcgr.vcf 3: chr5 38502681 38502681 C A p010_tumor-52fccd-somatic.pcgr.vcf 4: chr6 89951675 89951675 C T p010_tumor-52fccd-somatic.pcgr.vcf 5: chr7 82822603 82822603 G T p010_tumor-52fccd-somatic.pcgr.vcf

196698: chrX 15795073 15795073 A C SA533811_SP125786 196699: chrX 15800132 15800132 T A SA569276_SP133702 196700: chrX 15803607 15803607 G T SA558660_SP125807 196701: chr9 14398633 14398633 C G CGPA229 196702: chr1 186680291 186680291 C T CGPA234

str(ActiveDriverWGSInfo) List of 1 $ pdac:Classes 'data.table' and 'data.frame': 196702 obs. of 6 variables: ..$ chr : chr [1:196702] "chr3" "chr4" "chr5" "chr6" ... ..$ pos1 : num [1:196702] 1.20e+08 1.25e+08 3.85e+07 9.00e+07 8.28e+07 ... ..$ pos2 : num [1:196702] 1.20e+08 1.25e+08 3.85e+07 9.00e+07 8.28e+07 ... ..$ ref : chr [1:196702] "T" "G" "C" "C" ... ..$ alt : chr [1:196702] "C" "T" "A" "T" ... ..$ patient: chr [1:196702] "p010_tumor-52fccd-somatic.pcgr.vcf" "p010_tumor-52fccd-somatic.pcgr.vcf" "p010_tumor-52fccd-somatic.pcgr.vcf" "p010_tumor-52fccd-somatic.pcgr.vcf" ... ..- attr(*, ".internal.selfref")=

head(elements) chr start end id GENEID 20 chr12 912077 990053 RAD52 ENSG00000002016 30 chr17 38869859 38921770 LASP1 ENSG00000002834 56 chr12 21468911 21501669 RECQL ENSG00000004700 66 chr7 96120220 96322147 SLC25A13 ENSG00000004864 74 chr19 18831938 18868236 UPF1 ENSG00000005007 78 chr7 27181510 27185223 HOXA11 ENSG00000005073

I have also done some sanity checking on both mutation and elements data and found no issues with having NA's or empty values.

Can you please figure out why this might be producing an error? Many thanks.

— Reply to this email directly, view it on GitHub https://github.com/reimandlab/ActiveDriverWGSR/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7IXF3MWEK5L7C37ZU3YWZLJZAVCNFSM6AAAAABEIBYFCGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3TAMZWG4ZDGOA . You are receiving this because you were mentioned.Message ID: @.***>

skanwal commented 8 months ago

@reimand0 - I have emailed the data to your utoronto.ca id. Hopefully you have received it?

reimand0 commented 8 months ago

Hi Sehrish - received. I will reach out if i have questions. This may take a bit of time.

Jüri

On Mon, Mar 11, 2024 at 23:22 Sehrish Kanwal @.***> wrote:

@reimand0 https://github.com/reimand0 - I have emailed the data to your utoronto.ca id. Hopefully you have received it?

— Reply to this email directly, view it on GitHub https://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-1990005517, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7JT2QRKBDNBY2BAZO3YXZYITAVCNFSM6AAAAABEIBYFCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJQGAYDKNJRG4 . You are receiving this because you were mentioned.Message ID: @.***>

skanwal commented 8 months ago

Thanks, Juri. Looking forward to hearing back from you.

Best,

-- Dr. Sehrish Kanwal | Bioinformatics Scientist PhD, BS (Bioinformatics) University of Melbourne Centre for Cancer Research Victorian Comprehensive Cancer Centre Level 10, Room 10.2.T06 305 Grattan Street Melbourne, Victoria 3000 Australia M: +61 469 743 969 | E: @.**@.> research.unimelb.edu.au/umccrhttp://research.unimelb.edu.au/umccr | Twitter: @skanwal23 LinkedIn: https://www.linkedin.com/in/sehrish-kanwal-1b80bb42/

I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past and present.

From: reimand0 @.> Date: Wednesday, 13 March 2024 at 11:24 pm To: reimandlab/ActiveDriverWGSR @.> Cc: Sehrish Kanwal @.>, Author @.> Subject: Re: [reimandlab/ActiveDriverWGSR] Error in glm.fit: object fit not found (Issue #17) Hi Sehrish - received. I will reach out if i have questions. This may take a bit of time.

Jüri

On Mon, Mar 11, 2024 at 23:22 Sehrish Kanwal @.***> wrote:

@reimand0 https://github.com/reimand0 - I have emailed the data to your utoronto.ca id. Hopefully you have received it?

— Reply to this email directly, view it on GitHub https://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-1990005517, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7JT2QRKBDNBY2BAZO3YXZYITAVCNFSM6AAAAABEIBYFCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJQGAYDKNJRG4 . You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-1994267816, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACLGR2YFGZHGX3WOGWFWKHTYYBAP7AVCNFSM6AAAAABEIBYFCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJUGI3DOOBRGY. You are receiving this because you authored the thread.Message ID: @.***>

skanwal commented 7 months ago

Dear Juri,

Hope you’re doing well. Wondering if you had time to investigate the issue I had reported below?

Many thanks.

-- Dr. Sehrish Kanwal | Bioinformatics Scientist PhD, BS (Bioinformatics) University of Melbourne Centre for Cancer Research Victorian Comprehensive Cancer Centre Level 10, Room 10.2.T06 305 Grattan Street Melbourne, Victoria 3000 Australia M: +61 469 743 969 | E: @.**@.> research.unimelb.edu.au/umccrhttp://research.unimelb.edu.au/umccr | Twitter: @skanwal23 LinkedIn: https://www.linkedin.com/in/sehrish-kanwal-1b80bb42/

I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past and present.

From: Sehrish Kanwal @.> Date: Thursday, 14 March 2024 at 8:40 AM To: reimandlab/ActiveDriverWGSR @.> Subject: Re: [reimandlab/ActiveDriverWGSR] Error in glm.fit: object fit not found (Issue #17) Thanks, Juri. Looking forward to hearing back from you.

Best,

-- Dr. Sehrish Kanwal | Bioinformatics Scientist PhD, BS (Bioinformatics) University of Melbourne Centre for Cancer Research Victorian Comprehensive Cancer Centre Level 10, Room 10.2.T06 305 Grattan Street Melbourne, Victoria 3000 Australia M: +61 469 743 969 | E: @.**@.> research.unimelb.edu.au/umccrhttp://research.unimelb.edu.au/umccr | Twitter: @skanwal23 LinkedIn: https://www.linkedin.com/in/sehrish-kanwal-1b80bb42/

I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past and present.

From: reimand0 @.> Date: Wednesday, 13 March 2024 at 11:24 pm To: reimandlab/ActiveDriverWGSR @.> Cc: Sehrish Kanwal @.>, Author @.> Subject: Re: [reimandlab/ActiveDriverWGSR] Error in glm.fit: object fit not found (Issue #17) Hi Sehrish - received. I will reach out if i have questions. This may take a bit of time.

Jüri

On Mon, Mar 11, 2024 at 23:22 Sehrish Kanwal @.***> wrote:

@reimand0 https://github.com/reimand0 - I have emailed the data to your utoronto.ca id. Hopefully you have received it?

— Reply to this email directly, view it on GitHub https://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-1990005517, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7JT2QRKBDNBY2BAZO3YXZYITAVCNFSM6AAAAABEIBYFCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJQGAYDKNJRG4 . You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-1994267816, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACLGR2YFGZHGX3WOGWFWKHTYYBAP7AVCNFSM6AAAAABEIBYFCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJUGI3DOOBRGY. You are receiving this because you authored the thread.Message ID: @.***>

THT-sleepy commented 1 month ago

Hello, Skanwal

I've met exactly the same issue, is there any progression later?

Many thanks.

skanwal commented 1 month ago

Hello - @THT-sleepy

Unfortunately, no. I had shared the test data with the author as well but did't get a response.

reimand0 commented 1 month ago

Dear Sehrish & THT,

I am very sorry that this has been delayed. We are still on it with a number of other tasks for a bigger update of the algorithm. In the meantime, does your code work without specifying the recovery.dir?

all the best, Jüri

On Sun, Oct 6, 2024 at 04:13 Sehrish Kanwal @.***> wrote:

Hello - @THT-sleepy https://github.com/THT-sleepy

Unfortunately, no. I had shared the test data with the author as well but did't get a response.

— Reply to this email directly, view it on GitHub https://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-2395342589, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7PR6ZXFQESY3HZSASLZ2DWI3AVCNFSM6AAAAABPNC5YKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJVGM2DENJYHE . You are receiving this because you were mentioned.Message ID: @.***>

reimand0 commented 1 month ago

For what it's worth, ActiveDriverWGS works well for us in a number of applications and collaborations. I will let you know once we have a solution for this issue.

On Mon, Oct 7, 2024 at 06:09 Juri Reimand @.***> wrote:

Dear Sehrish & THT,

I am very sorry that this has been delayed. We are still on it with a number of other tasks for a bigger update of the algorithm. In the meantime, does your code work without specifying the recovery.dir?

all the best, Jüri

On Sun, Oct 6, 2024 at 04:13 Sehrish Kanwal @.***> wrote:

Hello - @THT-sleepy https://github.com/THT-sleepy

Unfortunately, no. I had shared the test data with the author as well but did't get a response.

— Reply to this email directly, view it on GitHub https://github.com/reimandlab/ActiveDriverWGSR/issues/17#issuecomment-2395342589, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7PR6ZXFQESY3HZSASLZ2DWI3AVCNFSM6AAAAABPNC5YKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJVGM2DENJYHE . You are receiving this because you were mentioned.Message ID: @.***>

THT-sleepy commented 1 month ago

Dear Sehrish & THT, I am very sorry that this has been delayed. We are still on it with a number of other tasks for a bigger update of the algorithm. In the meantime, does your code work without specifying the recovery.dir? all the best, Jüri … On Sun, Oct 6, 2024 at 04:13 Sehrish Kanwal @.> wrote: Hello - @THT-sleepy https://github.com/THT-sleepy Unfortunately, no. I had shared the test data with the author as well but did't get a response. — Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETAF7PR6ZXFQESY3HZSASLZ2DWI3AVCNFSM6AAAAABPNC5YKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJVGM2DENJYHE . You are receiving this because you were mentioned.Message ID: @.>

Dear Juri,

I didn't specify the recovery.dir.

best Huatao

skanwal commented 1 month ago

Thanks, Juri. I had also tried with and without recovery.dir. Both errored out with the same issue. Looking forward to the algorithm update. Please keep us posted.

THT-sleepy commented 1 month ago

For what it's worth, ActiveDriverWGS works well for us in a number of applications and collaborations. I will let you know once we have a solution for this issue. … On Mon, Oct 7, 2024 at 06:09 Juri Reimand @.> wrote: Dear Sehrish & THT, I am very sorry that this has been delayed. We are still on it with a number of other tasks for a bigger update of the algorithm. In the meantime, does your code work without specifying the recovery.dir? all the best, Jüri On Sun, Oct 6, 2024 at 04:13 Sehrish Kanwal @.> wrote: > Hello - @THT-sleepy https://github.com/THT-sleepy > > Unfortunately, no. I had shared the test data with the author as well but > did't get a response. > > — > Reply to this email directly, view it on GitHub > <#17 (comment)>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/AETAF7PR6ZXFQESY3HZSASLZ2DWI3AVCNFSM6AAAAABPNC5YKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJVGM2DENJYHE > . > You are receiving this because you were mentioned.Message ID: > @.***> >

Dear Juri,

I found a post(https://stackoverflow.com/questions/53476056/how-to-fix-error-in-glim-fit-fitnot-found-in-gamlss-regression) discussing a similar error, and based on my understanding of the post, it is possible that the version of stats we are using is different from yours(It seems that the error is caused by the use of the stats::glm function at lines 283-284 in ADWGS_test.R), which may have caused this error (someone mentioned that it fails on one computer but not on another). So, I would like to know if you can provide a conda environment.yml file, so that I can check whether this is the cause of the error. Thank you.

all the best, Huatao