Error in glm.fit: object fit not found #17
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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")=<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 figure out why this might be producing an error?
Many thanks.
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@reimand0 - I have emailed the data to your |
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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?
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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/umccr<http://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?
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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/umccr<http://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/umccr<http://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?
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Hello, Skanwal I've met exactly the same issue, is there any progression later? Many thanks. |
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Hello - @THT-sleepy Unfortunately, no. I had shared the test data with the author as well but did't get a response. |
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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.
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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.
>
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Dear Juri, I didn't specify the recovery.dir. best |
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Thanks, Juri. I had also tried with and without recovery.dir. Both errored out with the same issue. |
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, |
Hi @reimand0 ,
I am getting an error, when trying to run ActiveDriveWGS using following command:
The error is:
Data
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.
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