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mskilab-org / JaBbA

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
MIT License
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Difficulty installing the package(s) #33

Closed alhafidzhamdan closed 3 years ago

alhafidzhamdan commented 3 years ago

Hi there, congrats on a wonderful piece of work- I can see there's a lot of work being put into this. Amazing stuff.

I've had issues installing the JaBbA package. CPLEX installation seems OK however for the actual package, it always seems to throw error on dependencies. I've tried using a fresh R installation, a fresh conda installation etc. And i've tried Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE) also Still not managed to install to completion (same applies for fragCounter).

I wonder if somebody can hold my hand and help me install it. I'm running linux on a computer cluster. I've previously installed fishHook on my macbook and that works OK. I'm aware you're currently doing a workflow best practice so would be good to troubleshoot that.

Many thanks in advance! And once again congrats! A

xtYao commented 3 years ago

Hi,

What is the R enviorment you are using (aka sessionInfo())? We currently test in R3.6.1.

Xiaotong

alhafidzhamdan commented 3 years ago

Hi it's 

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Scientific Linux 7.5 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /gpfs/igmmfs01/eddie/WGS/anaconda/envs/Jabba/lib/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] magrittr_1.5      usethis_1.6.3     devtools_2.3.2    pkgload_1.1.0    
 [5] R6_2.4.1          rlang_0.4.8       fansi_0.4.1       tcltk_3.6.1      
 [9] tools_3.6.1       pkgbuild_1.1.0    sessioninfo_1.1.1 cli_2.1.0        
[13] git2r_0.27.1      withr_2.3.0       ellipsis_0.3.1    remotes_2.2.0    
[17] assertthat_0.2.1  digest_0.6.26     rprojroot_1.3-2   crayon_1.3.4     
[21] processx_3.4.4    callr_3.5.1       fs_1.5.0          ps_1.4.0         
[25] curl_4.3          testthat_2.3.2    memoise_1.1.0     glue_1.4.2       
[29] compiler_3.6.1    desc_1.2.0        backports_1.1.10  prettyunits_1.1.1

Here's some of the error logs:


ERROR: dependency ‘sequenza’ is not available for package ‘JaBbA’
* removing ‘/gpfs/igmmfs01/eddie/WGS/anaconda/envs/Jabba/lib/R/library/JaBbA’
Warning messages:
1: package ‘copynumber’ is not available (for R version 3.6.1) 
2: In i.p(...) :
  installation of package ‘sequenza’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/tmp/RtmpBzcZ71/file640f4669f3f6e/JaBbA_0.0.0.9000.tar.gz’ had non-zero exit status
alhafidzhamdan commented 3 years ago

Hi,

I started again from scratch this time, within a conda environment and R=3.6.1, and building the JaBbA R package with R CMD build and R CMD INSTALL. And I installed the dependencies that threw off error ie sequenza etc using conda. It seems to work but it's throwing an invalid file error.

(Jabba) [ahamdan@node2f24(eddie) extdata]$ ./jba junctions.vcf coverage.txt 
Did not find hets file  setting to NULL
Did not find nseg file  setting to NULL
JaBbA 2020-10-22 17:27:00: Found CPLEX environment in: /exports/igmm/eddie/WGS/scripts/JaBbA/

 _____         ___    _      _____ 
(___  )       (  _`\ ( )    (  _  )
    | |   _ _ | (_) )| |_   | (_) |
 _  | | /'_` )|  _ <'| '_`\ |  _  |
( )_| |( (_| || (_) )| |_) )| | | |
`\___/'`\__,_)(____/'(_,__/'(_) (_)

(Junction     Balance     Analysis)

JaBbA 2020-10-22 17:27:00: Located junction file junctions.vcf
JaBbA 2020-10-22 17:27:00: Located coverage file coverage.txt
JaBbA 2020-10-22 17:27:00: Loading packages ...
JaBbA 2020-10-22 17:27:00: Starting analysis in /gpfs/igmmfs01/eddie/WGS/scripts/JaBbA/inst/extdata
JaBbA 2020-10-22 17:27:00: ALT field format like BND
JaBbA 2020-10-22 17:27:01: Read in 83 total input junctions
JaBbA 2020-10-22 17:27:01: There are 0 tier 1 junctinos; 15 tier 2 junctinos; 68 tier 3 junctinos.
JaBbA 2020-10-22 17:27:01: Read in 26,625 5001bp bins of coverage data across 2 chromosomes
JaBbA 2020-10-22 17:27:01: Using previous segmentation found in jabba directory
JaBbA 2020-10-22 17:27:01: Loaded 15 junctions from the input.
JaBbA 2020-10-22 17:27:01: Found tier field enforcing >=1 CN at 0 junctions
JaBbA 2020-10-22 17:27:01: Removing 0 tier 3 junctions
JaBbA 2020-10-22 17:27:01: 2 INDEL-like isolated events
JaBbA 2020-10-22 17:27:01: 2 INDEL-like isolated junctions mandatorily EXCLUDED in the final model
JaBbA 2020-10-22 17:27:01: Conform the reference sequence length of: seg, coverage, and ra, to be: 
    16:90354753
    19:59128983
JaBbA 2020-10-22 17:27:01: Did not find nseg file! Ignore.
JaBbA 2020-10-22 17:27:03: Definining coverage good quality nodes as 10% bases covered by non-NA and non-Inf values in +/-100KB region
JaBbA 2020-10-22 17:27:03: Hard setting 4.825004 Mb of the genome to NA that didn't pass our quality threshold
JaBbA 2020-10-22 17:27:03: Using loess to fit mean to variance relationship in segments with greater than 5 bins
Error in file.exists(het.file) : invalid 'file' argument
Calls: suppressPackageStartupMessages ... JaBbA -> jabba_stub -> karyograph_stub -> file.exists
In addition: Warning messages:
1: multiple methods tables found for ‘seqinfo<-’ 
2: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘gGnome’ 
3: replacing previous import ‘GenomicRanges::score’ by ‘fishHook::score’ when loading ‘gGnome’ 
4: replacing previous import ‘GenomicRanges::seqinfo<-’ by ‘gTrack::seqinfo<-’ when loading ‘gGnome’ 
5: replacing previous import ‘Matrix::%&%’ by ‘gUtils::%&%’ when loading ‘gGnome’ 
6: replacing previous import ‘GenomicRanges::union’ by ‘igraph::union’ when loading ‘gGnome’ 
7: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘gGnome’ 
8: multiple methods tables found for ‘%&%’ 
9: In hg_seqlengths() :
  hg_seqlengths: supply genome seqlengths or set default with env variable DEFAULT_GENOME (e.g. Sys.setenv(DEFAULT_GENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens").  DEFAULT_BSGENOME can also be set to a path or URL of a tab delimited text *.chrom.sizes file
10: In jabba_stub(junctions = ra.all, seg = seg, coverage = coverage,  :
  hets file "NULL" not found, ignoring hets

Execution halted
xtYao commented 3 years ago

Hi,

Glad to hear it installed. I will fix this file error today.

Xiaotong

From: alhafidzhamdan notifications@github.com Sent: Friday, October 23, 2020 1:56 AM To: mskilab/JaBbA JaBbA@noreply.github.com Cc: Xiaotong Yao xiaotong.yao23@gmail.com; Assign assign@noreply.github.com Subject: Re: [mskilab/JaBbA] Difficulty installing the package(s) (#33)

Hi,

I started again from scratch this time, within a conda environment and R=3.6.1, and building the JaBbA R package with R CMD build and R CMD INSTALL. And I installed the dependencies that threw off error ie sequenza etc using conda. It seems to work but it's throwing an invalid file error.

(Jabba) [ahamdan@node2f24(eddie) extdata]$ ./jba junctions.vcf coverage.txt

Did not find hets file setting to NULL

Did not find nseg file setting to NULL

JaBbA 2020-10-22 17:27:00: Found CPLEX environment in: /exports/igmm/eddie/WGS/scripts/JaBbA/

(__ ) ( `\ ( ) ( _ )

| |   _ _ | (_) )| |_   | (_) |

| | /')| _ <'| '_\ | _ |

( )| |( (| || () )| |) )| | | |

\___/'_,)(_/'(,/'() ()

(Junction Balance Analysis)

JaBbA 2020-10-22 17:27:00: Located junction file junctions.vcf

JaBbA 2020-10-22 17:27:00: Located coverage file coverage.txt

JaBbA 2020-10-22 17:27:00: Loading packages ...

JaBbA 2020-10-22 17:27:00: Starting analysis in /gpfs/igmmfs01/eddie/WGS/scripts/JaBbA/inst/extdata

JaBbA 2020-10-22 17:27:00: ALT field format like BND

JaBbA 2020-10-22 17:27:01: Read in 83 total input junctions

JaBbA 2020-10-22 17:27:01: There are 0 tier 1 junctinos; 15 tier 2 junctinos; 68 tier 3 junctinos.

JaBbA 2020-10-22 17:27:01: Read in 26,625 5001bp bins of coverage data across 2 chromosomes

JaBbA 2020-10-22 17:27:01: Using previous segmentation found in jabba directory

JaBbA 2020-10-22 17:27:01: Loaded 15 junctions from the input.

JaBbA 2020-10-22 17:27:01: Found tier field enforcing >=1 CN at 0 junctions

JaBbA 2020-10-22 17:27:01: Removing 0 tier 3 junctions

JaBbA 2020-10-22 17:27:01: 2 INDEL-like isolated events

JaBbA 2020-10-22 17:27:01: 2 INDEL-like isolated junctions mandatorily EXCLUDED in the final model

JaBbA 2020-10-22 17:27:01: Conform the reference sequence length of: seg, coverage, and ra, to be: 

    16:90354753

    19:59128983

JaBbA 2020-10-22 17:27:01: Did not find nseg file! Ignore.

JaBbA 2020-10-22 17:27:03: Definining coverage good quality nodes as 10% bases covered by non-NA and non-Inf values in +/-100KB region

JaBbA 2020-10-22 17:27:03: Hard setting 4.825004 Mb of the genome to NA that didn't pass our quality threshold

JaBbA 2020-10-22 17:27:03: Using loess to fit mean to variance relationship in segments with greater than 5 bins

Error in file.exists(het.file) : invalid 'file' argument

Calls: suppressPackageStartupMessages ... JaBbA -> jabba_stub -> karyograph_stub -> file.exists

In addition: Warning messages:

1: multiple methods tables found for ‘seqinfo<-’

2: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘gGnome’

3: replacing previous import ‘GenomicRanges::score’ by ‘fishHook::score’ when loading ‘gGnome’

4: replacing previous import ‘GenomicRanges::seqinfo<-’ by ‘gTrack::seqinfo<-’ when loading ‘gGnome’

5: replacing previous import ‘Matrix::%&%’ by ‘gUtils::%&%’ when loading ‘gGnome’

6: replacing previous import ‘GenomicRanges::union’ by ‘igraph::union’ when loading ‘gGnome’

7: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘gGnome’

8: multiple methods tables found for ‘%&%’

9: In hg_seqlengths() :

hg_seqlengths: supply genome seqlengths or set default with env variable DEFAULT_GENOME (e.g. Sys.setenv(DEFAULT_GENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens"). DEFAULT_BSGENOME can also be set to a path or URL of a tab delimited text *.chrom.sizes file

10: In jabba_stub(junctions = ra.all, seg = seg, coverage = coverage, :

hets file "NULL" not found, ignoring hets

Execution halted

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xtYao commented 3 years ago

Should be fixed now https://github.com/mskilab/JaBbA/tree/6df1ad5c332bbdb602ada82e3c949b8f22ee002e

alhafidzhamdan commented 3 years ago

Hi @xtYao - Still not working I'm afraid - 


./jba junctions.vcf coverage.txt 
Did not find hets file  setting to NULL
Did not find nseg file  setting to NULL
JaBbA 2020-10-24 09:15:11: Found CPLEX environment in: /exports/igmm/eddie/WGS/scripts/cplex

 _____         ___    _      _____ 
(___  )       (  _`\ ( )    (  _  )
    | |   _ _ | (_) )| |_   | (_) |
 _  | | /'_` )|  _ <'| '_`\ |  _  |
( )_| |( (_| || (_) )| |_) )| | | |
`\___/'`\__,_)(____/'(_,__/'(_) (_)

(Junction     Balance     Analysis)

JaBbA 2020-10-24 09:15:11: Located junction file junctions.vcf
JaBbA 2020-10-24 09:15:11: Located coverage file coverage.txt
JaBbA 2020-10-24 09:15:11: Loading packages ...
JaBbA 2020-10-24 09:15:12: Starting analysis in /gpfs/igmmfs01/eddie/WGS/scripts/JaBbA/inst/extdata
JaBbA 2020-10-24 09:15:12: ALT field format like BND
JaBbA 2020-10-24 09:15:12: Read in 83 total input junctions
JaBbA 2020-10-24 09:15:12: There are 0 tier 1 junctinos; 15 tier 2 junctinos; 68 tier 3 junctinos.
JaBbA 2020-10-24 09:15:12: Read in 26,625 5001bp bins of coverage data across 2 chromosomes
JaBbA 2020-10-24 09:15:12: Using previous segmentation found in jabba directory
JaBbA 2020-10-24 09:15:12: Loaded 15 junctions from the input.
JaBbA 2020-10-24 09:15:13: Found tier field enforcing >=1 CN at 0 junctions
JaBbA 2020-10-24 09:15:13: Removing 0 tier 3 junctions
JaBbA 2020-10-24 09:15:13: 2 INDEL-like isolated events
JaBbA 2020-10-24 09:15:13: 2 INDEL-like isolated junctions mandatorily EXCLUDED in the final model
JaBbA 2020-10-24 09:15:13: Conform the reference sequence length of: seg, coverage, and ra, to be: 
    16:90354753
    19:59128983
    1:249250621
    2:243199373
    3:198022430
    4:191154276
    5:180915260
    6:171115067
    7:159138663
    8:146364022
    9:141213431
    10:135534747
    11:135006516
    12:133851895
    13:115169878
    14:107349540
    15:102531392
    17:81195210
    18:78077248
    20:63025520
    21:48129895
    22:51304566
    X:155270560
    Y:59373566
    MT:16569
JaBbA 2020-10-24 09:15:15: Definining coverage good quality nodes as 10% bases covered by non-NA and non-Inf values in +/-100KB region
JaBbA 2020-10-24 09:15:15: Hard setting 2951.035249 Mb of the genome to NA that didn't pass our quality threshold
JaBbA 2020-10-24 09:15:15: WARNING: more than half of the whole genome is set to NA, and ignored by JaBbA!!
JaBbA 2020-10-24 09:15:15: Using loess to fit mean to variance relationship in segments with greater than 5 bins
Error in file.exists(het.file) : invalid 'file' argument
Calls: suppressPackageStartupMessages ... JaBbA -> jabba_stub -> karyograph_stub -> file.exists
In addition: Warning messages:
1: multiple methods tables found for ‘seqinfo<-’ 
2: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘gGnome’ 
3: replacing previous import ‘GenomicRanges::score’ by ‘fishHook::score’ when loading ‘gGnome’ 
4: replacing previous import ‘GenomicRanges::seqinfo<-’ by ‘gTrack::seqinfo<-’ when loading ‘gGnome’ 
5: replacing previous import ‘Matrix::%&%’ by ‘gUtils::%&%’ when loading ‘gGnome’ 
6: replacing previous import ‘GenomicRanges::union’ by ‘igraph::union’ when loading ‘gGnome’ 
7: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘gGnome’ 
8: multiple methods tables found for ‘%&%’ 
9: In chr2num(V(G)$chrom) : NAs introduced by coercion
Execution halted
xtYao commented 3 years ago

Looking into this

xtYao commented 3 years ago

Would mind trying this again? https://github.com/mskilab/JaBbA/commit/c5edfb02b28d737a8acb564b1f724ee29a7c179d Thank you so much!

alhafidzhamdan commented 3 years ago

Works now. Thank you. However - output files that I got (from testing the example datasets) do not contain these file names: jabba.simple.gg.rds and jabba.seg.txt

Although i do have jabba.seg (without txt)- for this one probably just nomenclature but i am missing the jabba.simple.gg.rds

xtYao commented 3 years ago

Works now. Thank you. However - output files that I got (from testing the example datasets) do not contain these file names: jabba.simple.gg.rds and jabba.seg.txt

Although i do have jabba.seg (without txt)- for this one probably just nomenclature but i am missing the jabba.simple.gg.rds

That's different from what I got when running the example command. 

$ ls *jabba.simple.gg.rds                                                                                                                                                                                                                                                                                                                                                                          
jabba.simple.gg.rds

Could you make sure that run was finished correctly with these following lines printed on the screen?

JaBbA 2020-10-26 08:36:33: simplifying segments in JaBbA graph but keeping all edges (including copy 0), dumping to jabba.rds                                                                                                      
JaBbA 2020-10-26 08:36:34: Checking for hets                                                                                                                                                                                       
JaBbA 2020-10-26 08:36:36: Loose end quality annotated                                                                                                                                                                             
JaBbA 2020-10-26 08:36:36: Saving results                                                                                                                                                                                          
JaBbA 2020-10-26 08:36:40: Generating figures                                                                                                                                                                                      
JaBbA 2020-10-26 08:36:46: Done .. job output in:
alhafidzhamdan commented 3 years ago

Thanks- it is working now. Turns out I didn't follow the instructions to the T.

I then went on and installed fragCounter, and liftover the gc1000.rds and map1000.rds files to hg38 to be used in fragCounter and I got some error there also. I've raised the issue here https://github.com/mskilab/fragCounter/issues/7

Thanks for your support so far!

xtYao commented 3 years ago

Thank you for helping us spot all these bugs! I’ll close this now and move on to iron out the fragCounter issues.

Get Outlook for iOShttps://aka.ms/o0ukef

From: alhafidzhamdan notifications@github.com Sent: Tuesday, October 27, 2020 1:58:16 PM To: mskilab/JaBbA JaBbA@noreply.github.com Cc: Xiaotong Yao xiaotong.yao23@gmail.com; State change state_change@noreply.github.com Subject: Re: [mskilab/JaBbA] Difficulty installing the package(s) (#33)

Thanks- it is working now. Turns out I didn't follow the instructions to the T.

I then went on and installed fragCounter, and liftover the gc1000.rds and map1000.rds files to hg38 to be used in fragCounter and I got some error there also. I've raised the issue here mskilab/fragCounter#7https://github.com/mskilab/fragCounter/issues/7

Thanks for your support so far!

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/mskilab/JaBbA/issues/33#issuecomment-717420328, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABVYZHKTTZ2OXDBSEE7CRDDSM4C3RANCNFSM4SV6KDCQ.