getFeatureRangers error

[susheelbhanu]

Hi,

Thanks for making the workflow publicly available. I'm trying to run a test dataset and getting the following error(s):

Error in rule eisar_ranges:
    jobid: 29
    output: results/eisar/GRCh38.p13/GRCh38.p13.ranges.rds
    log: results/eisar/GRCh38.p13/GRCh38.p13.ranges.out, results/eisar/GRCh38.p13/GRCh38.p13.ranges.err (check log file(s) for error message)
    conda-env: /mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/.snakemake/conda/336b4d3ff693c764dcc44de6b60b8999

RuleException:
CalledProcessError in line 21 of /mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/workflow/rules/eisar.smk:
Command 'source /scratch/users/sbusi/tools/miniconda3/bin/activate '/mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/.snakemake/conda/336b4d3ff693c764dcc44de6b60b8999'; set -euo pipefail;  Rscript --vanilla /mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/.snakemake/scripts/tmpkayhz1p2.eisar_ranges.R' returned non-zero exit status 1.

The log file has the following message:

Error in getFeatureRanges(gtf = input$gtf, featureType = c("spliced",  :
  getFeatureRanges() requires installing the Bioconductor package 'GenomicFeatures' using BiocManager::install("GenomicFeatures")
Calls: main -> getFeatureRanges
Execution halted

any idea why this might be the case?

Thank you, Susheel

[ghost]

Hey Susheel,

Could you show me how you are running the workflow? Each workflow step has an associated conda environment file which lists the bioconductor package dependencies. When you run Snakemake with the --use-conda flag it should instruct Snakemake to install all the required dependencies. If the GenomicFeatures package is not installed it could be an issue with the conda recipe for the eisaR package. Alternatively, you could edit the conda environment file for that particular step of the workflow and explicitly include the GenomicFeatures package as a dependency. For example:

name: eisar
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bioconductor-eisar
  - bioconductor-genomicfeatures

Thanks, James

[susheelbhanu]

Hey James,

Thanks for the quick response. This is my launcher script:

conda activate scrna
snakemake --use-conda --cores all -rp

Will try with the updated conda env and keep you posted.

Thank you!

[susheelbhanu]

Hi James,

That seems to have fixed the earlier issue, but now I'm running into another:

Error in rule busparse_get_velocity_files:
    jobid: 4
    output: results/busparse/get_velocity_files/GRCh38.p13/cDNA_introns.fa, results/busparse/get_velocity_files/GRCh38.p13/cDNA_tx_to_capture.txt, results/busparse/get_velocity_files/GRCh38.p13/introns_tx_to_capture.txt, results/busparse/get_velocity_files/GRCh38.p13/tr2g.tsv
    log: results/busparse/get_velocity_files/GRCh38.p13/log.out, results/busparse/get_velocity_files/GRCh38.p13/log.err (check log file(s) for error message)
    conda-env: /mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/.snakemake/conda/56cdea1a510b86f6ec678e539112c479

RuleException:
CalledProcessError in line 27 of /mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/workflow/rules/busparse.smk:
Command 'source /scratch/users/sbusi/tools/miniconda3/bin/activate '/mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/.snakemake/conda/56cdea1a510b86f6ec678e539112c479'; set -euo pipefail;  Rscript --vanilla /mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/.snakemake/scripts/tmpg_ugt7wz.get_velocity_files.R' returned non-zero exit status 1.
  File "/mnt/lscratch/users/sbusi/aaron_MG_MT/scrna/workflow/rules/busparse.smk", line 27, in __rule_busparse_get_velocity_files
  File "/scratch/users/sbusi/tools/miniconda3/envs/scrna/lib/python3.10/concurrent/futures/thread.py", line 58, in run

The log file suggests an issue with one of the libraries

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

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

    strsplit

Assuming that all chromosomes are linenar.
Error: 'new2old' not supported in 'seqinfo<-,DNAStringSet-method'
Execution halted

Thank you!

P.S. Just created this as well: https://github.com/Bioconductor/GenomeInfoDb/issues/34