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Sequenza User Group

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Welcome to Sequenza User Group!!
Feel free to ask questions and expose your problems/difficulties using sequenza.
Proposal and ideas are welcome as well.

Enjoy!!

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Amit Goyal, … Tom Clark21

Feb 18

Error in seq.default(from = 1, to = CNt, by = 1) : 'to' cannot be NA, NaN or infinite

https://t.me/+QhvBEnNvJBpmNDFk These DMT carts come filled with 250mg of N, N-Dimethyltryptamine (DMT

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Error in seq.default(from = 1, to = CNt, by = 1) : 'to' cannot be NA, NaN or infinite

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Feb 18

Feb 16

Unusual reports on dmt powdered cartridges

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Unusual reports on dmt powdered cartridges

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Feb 16

Feb 4

Best vapes dmt productions 2026

Preliminary research suggests N,N-dimethyltryptamine (DMT) has potential therapeutic benefits for a

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Best vapes dmt productions 2026

Preliminary research suggests N,N-dimethyltryptamine (DMT) has potential therapeutic benefits for a

Feb 4

Jan 31

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Preliminary research suggests N,N-dimethyltryptamine (DMT) has potential therapeutic benefits for a

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Buy: "DMT VAPES/DMT CARTS" @teziland)telegram

Preliminary research suggests N,N-dimethyltryptamine (DMT) has potential therapeutic benefits for a

Jan 31

Jan 31

Home: "DMT CARTS/DMT VAPES"

Preliminary research suggests N,N-dimethyltryptamine (DMT) has potential therapeutic benefits for a

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Preliminary research suggests N,N-dimethyltryptamine (DMT) has potential therapeutic benefits for a

Jan 31

Francesco Favero

Jan 27

Spam issue in Google Groups

Dear all, I really apologize for my slow reply here, things are not helped by the considerable amount

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Spam issue in Google Groups

Dear all, I really apologize for my slow reply here, things are not helped by the considerable amount

Jan 27

12/16/25

seqz_binning not reducing file size with high-coverage WGS data (>150x) + segmentation fault

Hello, I'm experiencing issues with sequenza-utils on high-coverage whole-genome sequencing data

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seqz_binning not reducing file size with high-coverage WGS data (>150x) + segmentation fault

Hello, I'm experiencing issues with sequenza-utils on high-coverage whole-genome sequencing data

12/16/25

Davide Cittaro, Michael Knudsen5

5/15/25

Memory error (paste exceeding 2^31-1 bytes)

I have had the same issue (it happens for noisy samples), and I've located the problem to this

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Memory error (paste exceeding 2^31-1 bytes)

I have had the same issue (it happens for noisy samples), and I've located the problem to this

5/15/25

virginia gazziero

5/13/25

Errors including r-sequenza in bioconda recipe

Hi, Thanks for the package! I am currently working at the development of a nf-core pipeline, and to

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Errors including r-sequenza in bioconda recipe

Hi, Thanks for the package! I am currently working at the development of a nf-core pipeline, and to

5/13/25

NILESH MUKHERJEE, Francesco Favero2

3/19/25

Sequenza v4.0.0 Error/Issue Debugging help required

Hi Nilesh, I've messed up adding some optimization working only in my laptop, which uses clang to

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Sequenza v4.0.0 Error/Issue Debugging help required

Hi Nilesh, I've messed up adding some optimization working only in my laptop, which uses clang to

3/19/25

2/8/25

How to use sequenza to detect focal homozygous deletions

Hi, I am preparing to work on a project to call CNV events in a number of WES tumor -normal pairs.

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How to use sequenza to detect focal homozygous deletions

Hi, I am preparing to work on a project to call CNV events in a number of WES tumor -normal pairs.

2/8/25

Michael Knudsen2

11/28/24

Corner case bug in sequenza.results?

Hi, Quick update on this issue. I have managed to get around it by adding seg.tab <- seg.tab[seg.

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Corner case bug in sequenza.results?

Hi, Quick update on this issue. I have managed to get around it by adding seg.tab <- seg.tab[seg.

11/28/24

Tusharika Rastogi

11/11/24

Sequenza.extract ERROR

Hello, I am trying to use the sequenza.extract function to process the seqz data. I produced the seqz

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Sequenza.extract ERROR

Hello, I am trying to use the sequenza.extract function to process the seqz data. I produced the seqz

11/11/24

Fenisha Shah, favero.f...@gmail.com3

6/27/24

Installation error with the latest version of sequenza

Hello Francesco That seems to work! Thank you for your prompt response. I would like to highlight

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Installation error with the latest version of sequenza

Hello Francesco That seems to work! Thank you for your prompt response. I would like to highlight

6/27/24

6/22/24

Sequenza ERROR: Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)

Hi I am using Sequenza to identify CNAs in tumor-normal files . A year ago I was able to generate the

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Sequenza ERROR: Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)

Hi I am using Sequenza to identify CNAs in tumor-normal files . A year ago I was able to generate the

6/22/24

6/14/24

Unable to install sequenza on any version of R.

install.packages('sequenza') will not work after multiple tries on various distros. Any ideas

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Unable to install sequenza on any version of R.

install.packages('sequenza') will not work after multiple tries on various distros. Any ideas

6/14/24

rkendar, … Michael Knudsen6

6/12/24

Sequenza failed >100 GB RAM

Yup, it works fine. I'm running it in production without any issues. I'm using a conda

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Sequenza failed >100 GB RAM

Yup, it works fine. I'm running it in production without any issues. I'm using a conda

6/12/24

Xin Zheng, … satishkumar Ranganathan Ganakammal4

5/30/24

equenza.extract error

Hello , Did any one solve this issue ? if so please provide any insights on the same Regards, Satish

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equenza.extract error

Hello , Did any one solve this issue ? if so please provide any insights on the same Regards, Satish

5/30/24

Giorgia Gandolfi, Davide Cittaro2

5/29/24

bam2seqz only processes one chromosome

Do the two input file have the same chromosome order? I had similar issue recently and realized that

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bam2seqz only processes one chromosome

Do the two input file have the same chromosome order? I had similar issue recently and realized that

5/29/24

Michael Knudsen

5/29/24

Adjusted depth ratios before segmentation

Hi, Is it possible to make Sequenza output adjusted depth ratios at all SNP positions before

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Adjusted depth ratios before segmentation

Hi, Is it possible to make Sequenza output adjusted depth ratios at all SNP positions before

5/29/24

Jimin Hwang, Minyi2

5/13/24

gc_wiggle takes too much time

I'm having this issue as well - did you ever find a solution? On Thursday, August 17, 2023 at 8:

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gc_wiggle takes too much time

I'm having this issue as well - did you ever find a solution? On Thursday, August 17, 2023 at 8:

5/13/24

5/1/24

sequenza hg38 bins and blacklists

Dear group, I am a new user trying to use sequenza with hg38. I have had luck with the Sequenza_CNAqc

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sequenza hg38 bins and blacklists

Dear group, I am a new user trying to use sequenza with hg38. I have had luck with the Sequenza_CNAqc

5/1/24

4/10/24

R sequenza package installation error

Hi all, I am not able to install the R sequenza package to R 3.2.1 on macOS. It throws the following

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R sequenza package installation error

Hi all, I am not able to install the R sequenza package to R 3.2.1 on macOS. It throws the following

4/10/24

Eric Blanc, … Donkiss Zidane5

3/31/24

Error in gc.sample.stats

If you're interested in exploring the world of psychedelic mushrooms, you may be wondering if

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Error in gc.sample.stats

If you're interested in exploring the world of psychedelic mushrooms, you may be wondering if

3/31/24

3/5/24

Error in segmenting depth ratios

Hello, I'm trying to identify tumor purity from Strelka2 vcf output. Due to error issues in GC

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Error in segmenting depth ratios

Hello, I'm trying to identify tumor purity from Strelka2 vcf output. Due to error issues in GC

3/5/24

satishkumar Ranganathan Ganakammal, … Xiaoyan Luo5

12/24/23

Error while running sequenza

Hello, I am also trying to generated CNV and purity report for my data. Below is the command I am

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Error while running sequenza

Hello, I am also trying to generated CNV and purity report for my data. Below is the command I am

12/24/23

satishkumar Ranganathan Ganakammal2

12/23/23

Inferring Tumor purity (High or low)

Hello, I am not able to find relationship between cellularity and tumor purity from paper or the

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Inferring Tumor purity (High or low)

Hello, I am not able to find relationship between cellularity and tumor purity from paper or the

12/23/23

PRAKHAR SONIK, … Francesco Favero9

12/12/23

Empty seqz.gz output from bam2seqz

You can have a look at how we generate the seqz from variants here https://bitbucket.org/

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Empty seqz.gz output from bam2seqz

You can have a look at how we generate the seqz from variants here https://bitbucket.org/

12/12/23

Sequenza User Group

12/8/23

New sequenza version

Dear all, After loosing the copynumber package dependency (it was removed from BioC since

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New sequenza version

Dear all, After loosing the copynumber package dependency (it was removed from BioC since

12/8/23

8/20/23

Depth ratio of 0.5 - noisy data

Hi, I've been running the standard Sequenza pipeline and it works pretty well. For some of the

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Depth ratio of 0.5 - noisy data

Hi, I've been running the standard Sequenza pipeline and it works pretty well. For some of the

8/20/23

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