Open CicadaDennis opened 5 months ago
Additional info on run error. The rlseq log JL01_S1_R1_001_hg38__rlseq.log contains:
$Coverage
[1] "/N/scratch/scttest/Quartz/rlpipes_out/coverage/JL01_S1_R1_001_hg38.bw"
$Peaks
[1] "/N/scratch/scttest/Quartz/rlpipes_out/peaks/JL01_S1_R1_001_hg38.broadPeak"
$genome
[1] "hg38"
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
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
!anyNA(m32) is not TRUE
Calls: <Anonymous> ... .get_chrom_info_for_registered_UCSC_genome -> GET_CHROM_SIZES -> .order_seqlevels -> stopifnot
Execution halted
Hi @CicadaDennis I have now updated the code to address this issue by removing the fine-grained package versions as you suggested. Please install from pypi or from GitHub for now (currently awaiting the official release of v0.9.4 on bioconda). Please try this out and let me know if you have any issues!
Hello, In working with a researcher at Indiana University, we found that the conda installed RLPipes had errors when building the rlseq conda environment with snakemake. (See example error below) I discovered two places where changing one value in the environment file lib/python3.9/site-packages/rlpipes/src/envs/rlseq.yaml would fix specific failures: changed
but eventually modified the file by removing the =xxxxx values after the version numbers for a large number of the items in the file, to see if it would build the environment without those parts of the file.
Example error:
However, after successfully building the conda environments, the run of RLPipes still had an error in the rlseq section of the workflow:
Sincerely, Cicada Dennis