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wangjr03 / FLAMINGO

MIT License
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environments for FLAMINGO in conda #7

Closed feefee20 closed 1 year ago

feefee20 commented 1 year ago

Hello,

Thanks for the useful tool! I am trying to add your tool in conda. Would you please provide all dependencies/environments to stabilize your tool in conda? Thanks for your help.

Here's my environment in conda:

Python 3.7.0 | packaged by conda-forge | (default, Nov 12 2018, 20:15:55) [GCC 7.3.0] :: Anaconda, Inc. on linux

R version 3.5.1 (2018-07-02)

feefee20 commented 1 year ago

Hello, what version of mgcv is available for R3.5.1 ? The current mgcv seems to work in >= R3.6.0 (https://cran.r-project.org/web/packages/mgcv/index.html).

[solved] installed mgcv_1.8-33 (https://cran.r-project.org/src/contrib/Archive/mgcv/mgcv_1.8-33.tar.gz) that works in R3.5.1

feefee20 commented 1 year ago

Hi again,

I am trying to learn the tool by following your tutorial with the following commands and .hic file downloaded from your server: '4DNFI1UEG1HD.hic'.

It seemed to work for a while and stopped without any notice. I see the temp files intermediately generated by R script as below:

drwxr-xr-x 500 Nov 4 13:25 Domain_data drwxr-xr-x 251 Nov 4 13:25 Genomic_loc -rw-r--r-- 1577093727 Nov 4 13:26 tmp_IF.txt.gz -rw-r--r-- 1612126093 Nov 4 13:27 tmp_PD.txt.gz -rw-r--r-- 1070294 Nov 4 14:43 intra_domain.Rdata

Would you please help me out to fix the issue? Thanks again.

cat Flamingo.R library(FLAMINGOr) library(GenomicFeatures) library(Matrix) setwd("/home/usr/test/") all_size <- getChromInfoFromUCSC("hg38") chr_name='1' chr_name = as.numeric(chr_name) chr_size = all_size[chr_name,2] chr_name <- paste0('chr',chr_name) res = flamingo.main_func_large(hic_data_low='4DNFI1UEG1HD.hic', file_format='hic', domain_res=1e6,frag_res=5e3, chr_size=chr_size, chr_name=chr_name, normalization='KR', downsampling_rates=0.75, lambda=10,max_dist=0.01,nThread=10,n_row=30000)

cat R-Rout

Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min

Loading required package: S4Vectors Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

expand

Download and preprocess the 'chrominfo' data frame ... OK [1] "Contact map is too large, large matrix mod is on" [1] "Dividing domains..." [1] "Processing Fragments..." [1] "caching datasets..." x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table [1] "Reconstructing backbones..." Loading required package: nlme

Attaching package: ‘nlme’

The following object is masked from ‘package:IRanges’:

collapse

This is mgcv 1.8-30. For overview type 'help("mgcv-package")'. [1] "Reconstructing intra-domain structures..." [1] "Assembling structures..." [1] "Reading substructures..." [1] 0.9025089 [1] 0.89027 [1] 0.9137103 [1] 0.9374543 [1] 0.9477833 [1] 0.953385 [1] 0.9551066 [1] 0.9559585 [1] 0.9561721 [1] 0.9564341 [1] 0.9562101 [1] 0.9563441 [1] 0.9564717 [1] 0.9564755

Our system is under:

PRETTY_NAME="Debian GNU/Linux bookworm/sid" NAME="Debian GNU/Linux" VERSION_CODENAME=bookworm

JiaxinYangJX commented 1 year ago

Thanks for using our software!

I guess there might be version conflicts with the imported packages. Below are the specific versions we used. Let us know if it works or not. Thanks!

strawr_0.0.9 mgcv_1.8-24 data.table_1.14.2 Matrix_1.2-14

feefee20 commented 1 year ago

Hello, thanks for leaving your comments.

I tried to run with same input file using the specific versions you used. It was stopped in the same step: Would be there any other possibilities?

JiaxinYangJX commented 1 year ago

Hi, thanks for reaching out. Based on the output file, I think your code has been run successfully. Only thing is that you need to save the res data.

feefee20 commented 1 year ago

Thanks for checking. All set! Thanks again!