Error running bcbioRNASeq from within bcbio: there is no package called ‘bcbioRNASeq’ #3565
Comments
|
Hi @amizeranschi ! Thanks for testing and reporting! I am getting the below error now: @mjsteinbaugh could you please help us with this error? Sergey |
|
Hi Sergey yeah I'll take a look tonight. If you can post the R session info via |
|
Basically I just need to know which version of bcbioRNASeq, basejump, and AcidBase. For reference, relevant Python code is here: |
|
@amizeranschi What version of bcbio-nextgen are you running? Is this the latest development build? |
|
Yeah I think something weird may be going on with the conda environment in that bcbio install. Here's a clean install of the conda activate r-bcbiornaseq@0.3.42
RR.version.string
# [1] "R version 4.1.1 (2021-08-10)"
packageVersion("bcbioRNASeq")
# [1] ‘0.3.42’
packageVersion("basejump")
# [1] ‘0.14.22’
packageVersion("AcidBase")
# [1] ‘0.4.5’
suppressPackageStartupMessages({
library(bcbioRNASeq)
})
# Loads clean |
|
Ah OK the conda recipe issue appears to be in CloudBioLinux here: https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml#L272 Adjusting the bcbioRNASeq R package dependencies are defined in DESCRIPTION file here, for reference: https://github.com/hbc/bcbioRNASeq/blob/master/DESCRIPTION |
|
thanks @mjsteinbaugh !
My versions: |
|
@naumenko-sa Where's |
|
Ah nevermind got it, it's here: bcbio-nextgen/bcbio/rnaseq/bcbiornaseq.py Line 128 in 71c6f97 Yeah rename |
|
Thanks @mjsteinbaugh ! I've fixed that and rda -> rds The next issue is: Could you please take a look? Sergey |
|
Yeah for RDS files, use |
|
Another minor thing is that R 4.1 adds support for a native pipe |
|
Thanks @mjsteinbaugh ! Almost there! With these changes + I am getting: The sample sheet: The yaml template: details:
- analysis: RNA-seq
genome_build: hg38
algorithm:
quality_format: standard
aligner: false
strandedness: unstranded
tools_on:
- bcbiornaseq
- keep_gene_version
bcbiornaseq:
organism: homo sapiens
interesting_groups: category
upload:
dir: ../final
resources:
star:
cores: 10
memory: 10GThe basic tximport companion works ok: Sergey |
|
OK cool I'll take a look and see if we need to publish any fixes in the package |
|
@naumenko-sa Hi Sergey, following up on this, I'm working on a code update this week and will ping you back soon. |
|
Thanks a lot for looking into this. Please let me know if I can do anything to help with testing. |
|
@mjsteinbaugh sorry for bugging, any luck with the update? |
|
@naumenko-sa Yep totally, I'll work on fixing it this week ASAP. What's your timeline for the 1.2.9 release? |
|
thanks Michael! |
|
OK I'll work on fixing this today |
|
Can you send me a copy of the example data from |
|
Sure, uploading them here: https://www.dropbox.com/sh/w9ogvhbeqirluq4/AAB-YpjkbhgUP8YHpZOfV9sTa?dl=0 |
|
What's the R code that gets passed in the |
|
Ah OK think I may have it -- seems to be a situation where |
|
Here's the error with more verbosity, I'm working on a version bump that will fix this: |
|
Thanks Michael! |
|
Cool I think I have a working fix, will push an update to GitHub soon |
|
I'm working on some additional improvements to the package that we can table for a later release...this fix should work so you can push the bcbio-nextgen 1.2.9 update |
|
OK I think bcbioRNASeq v0.3.43 should fix this issue. I'm working on updating on bioconda. |
|
Thanks again for all your help so far. After upgrading to the latest development version and getting the sacCer3 data, the RNA-seq analysis progressed further for me, but still ended up crashing. Let me know if you want me to share a script with everything I'm doing here, in case it could help with reproducing and debugging. Here's the error I'm running into: |
|
Thanks @amizeranschi I see the problem there, and it appears to be specific to the sacCer3 genome: Can you post a copy of the The Best, |
|
I also need to add an update to exclude the This should return: This is handled by the |
|
Thanks for the reply @mjsteinbaugh I'm attaching the file you requested: I'm also attaching a file with the commands I used to set up bcbio, to download the data and to set up the bcbio runs. The relevant lines for this analysis are 115-166 (downloading the data) and 206-235 (setting up and running the analysis). Hope this helps. |
|
OK great thanks, I'll work on a fix for this over the weekend and will be in touch soon with an update. |
|
OK this tx2gene issue with the sacCer3 genome should be fixed by the pending update to See relevant code change here: https://github.com/acidgenomics/r-acidgenomes/blob/main/R/AllClasses.R#L864 You can check this with your install here: packageVersion("AcidGenomes")
## 0.2.20
library(AcidGenomes)
tx2gene <- importTx2Gene(
file = pasteURL(
"github.com",
"bcbio",
"bcbio-nextgen",
"files",
"7739401",
"tx2gene.csv",
protocol = "https"
)
)
print(tx2gene)
## Tx2Gene with 7036 rows and 2 columns
## txId geneId
## <character> <character>
## 1 ETS1-1_rRNA ETS1-1
## 2 ETS1-2_rRNA ETS1-2
## 3 ETS2-1_rRNA ETS2-1
## 4 ETS2-2_rRNA ETS2-2
## 5 HRA1_ncRNA HRA1
## ... ... ...
## 7032 YPR202W_mRNA YPR202W
## 7033 YPR203W_mRNA YPR203W
## 7034 YPR204C-A_mRNA YPR204C-A
## 7035 YPR204W_mRNA YPR204W
## 7036 ZOD1_ncRNA ZOD1 |
|
thanks @mjsteinbaugh! @amizeranschi please let us know if it works for you. |
|
Hello, Thanks for looking into this. I upgraded bcbio and tools to latest development and launched R from the directory However, the bcbio analysis still ended up crashing, this time due to the version of a different package: |
|
You're seeing this error because the conda environment solver isn't working correctly. We should be installing these versions: |
|
Could you pin these package versions as well in cloudbiolinux? |
|
I've added https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml#L281, please try again! |
|
Thanks, but that doesn't seem to be ebough to get everything installed as it should. You might have to pin all the 6 package versions mentioned above. |
|
please try again, I hope we got all of them now |
|
Thanks a lot. We're definitely making progress. This time, I have checked now and that GTF file doesn't have any header. It was installed as part of the sacCer3 genome by bcbio. |
|
Thanks @amizeranschi can you post that GTF file so I can take a look and work on a fix? |
|
Sure thing, here you go. I changed the extension to .txt so that GitHub would accept it. |
|
OK this appears to be fixed in the development version of |
|
Would you consider adding support in bcbiornaseq for differential affinity in ChIP-seq and ATAC-seq peaks? Given that bcbio produces consensus peaks and computes read counts, these could be used in DESeq2 exactly like in the RNA-seq scenario. https://bcbio-nextgen.readthedocs.io/en/latest/contents/atac.html#differential-affinity-analysis |
|
@amizeranschi OK I think this should be fixed on bioconda. |
|
Hello, |
|
Hi @Melisa-Magallanes thanks for the update -- I'll try clean installing bcbio and see if I can reproduce |
|
Just in case your error is similar to what I've been seeing ( Have a look here: bioconda/bioconda-recipes#36499 (comment) |
|
Thanks for the update! I'll see if we can come up with a fix in bioconda-recipes. |
|
Great, thanks a lot. Please have a look at Edit: I've submitted a couple of pull requests. |
|
@amizeranschi |
|
Thanks @mjsteinbaugh ! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hello!
I'm trying to run a bulk RNA-seq analysis using the following template:
However, this ends with the following error:
This is strange to see, because the package does seem to be installed in the
rbcbiornaseqenvironment:The text was updated successfully, but these errors were encountered: