I am also facing the same problem using C. Elegans genome from ensembl please help

Error in rule sizeFactors:
jobid: 21
output: uORFs/sfactors_lprot.csv
log: logs/sizeFactors.log (check log file(s) for error message)
conda-env: /home/ngslab/ashish/project/.snakemake/conda/5bc873a8
shell:
mkdir -p uORFs; uORF-Tools/scripts/generate_size_factors.R -t uORF-Tools/samples.tsv -b maplink/ -a uORFs/longest_protein_coding_transcripts.gtf -s uORFs/sfactors_lprot.csv 2> logs/sizeFactors.log;

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/ngslab/ashish/project/.snakemake/log/2020-04-04T005245.080262.snakemake.log

I also added ##format: gtf still it is not working

Hello,

I'm quite excited to use uORF-Tools. It seems to run fine at the beginning but I'm getting the following error after about 8% of jobs are done:

`[Wed May 15 09:22:47 2019]
rule sizeFactors:
input: uORFs/longest_protein_coding_transcripts.gtf, maplink/RIBO-ISRIB-1.bam, maplink/RIBO-ISRIB-2.bam, maplink/RIBO-ISRIB-3.bam, maplink/RIBO-vehicle-1.bam, maplink/RIBO-vehicle-2.bam, maplink/RIBO-vehicle-3.bam
output: uORFs/sfactors_lprot.csv
jobid: 21

Activating conda environment: /Users/mo/project/.snakemake/conda/54de1460
Loading required package: methods
Loading required package: stats4
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

Attaching package: ‘S4Vectors’

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

expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

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

colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

aperm, apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

type

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

strsplit

Loading required package: Rsamtools

Attaching package: ‘plyr’

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

compact

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

count

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

desc

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

rename

Error in while (grepl("^#", line)) { : argument is of length zero
Calls: import.gff ... import -> import -> import -> .local -> .sniffGFFVersion
Execution halted
[Wed May 15 09:23:03 2019]
Error in rule sizeFactors:
jobid: 21
output: uORFs/sfactors_lprot.csv
conda-env: /Users/mo/project/.snakemake/conda/54de1460
shell:
mkdir -p uORFs; uORF-Tools/scripts/generate_size_factors.R -t uORF-Tools/samples.tsv -b maplink/ -a uORFs/longest_protein_coding_transcripts.gtf -s uORFs/sfactors_lprot.csv;
`

I can't exactly seem to figure out why exactly the argument is of length zero in the grep function. What am I missing? I'm working with Mus musculus GRC38.92 Ensembl genome and corresponding gtf file.

Morgane

Hello,
I would like to run uORF-Tools with some ribo-seq maize data. I am a beginner when it comes to coding. I am using the LSF cluster to run it, so I modified my scripts according to that to the best of my abilities. The error I get when I run the script is:

Building DAG of jobs...
MissingInputException in line 4 of /group/lorri/uorfs/uORFtools/rules/bootstrap.smk:
Missing input files for rule rawbamlink:
SRR18584242.unique.bam

Based on the error message, I assuming the mistake is somewhere in the first few lines of the bootstrap.smk file. Here are the first few lines of that file:

def getbam(wildcards):
    return samples.loc[(wildcards.method, wildcards.condition, wildcards.replicate), ["/group/lorri/uorfs/uORFtools/inputFile"]].dropna()

rule rawbamlink:
    input:
	bams=getbam
    output:
	"/group/lorri/uorfs/uORFtools/maplink/{method}-{condition}-{replicate}.bam"
    params:
	inlink=lambda wildcards, input:(os.getcwd() + "/" + (os.path.splitext(input.bams[0])[0]) + ".bam"),
        outlink=lambda wildcards, output:(os.getcwd() + "/" + str(output))
    threads: 1
    shell:
	"mkdir -p /group/lorri/uorfs/uORFtools/maplink; ln -s {params.inlink} {params.outlink}"

Thanks for reading.

Hi, I am very excited about using uORF-tools along with snakemake and conda. I have followed the instruction for installation on ReadMe.md and the User Guide. While running

% snakemake --use-conda -s uORF-Tools/Snakefile --configfile uORF-Tools/config.yaml --directory ${PWD} -j 20 --latency-wait 60

I've encountered the error message:

AttributeError in line 33 of /Users/cwon2/CompBio/uORFs-project/uORF-Tools/Snakefile:
module 'collections' has no attribute 'Iterable'
  File "/Users/cwon2/CompBio/uORFs-project/uORF-Tools/Snakefile", line 33, in <module>

It comes to my attention that the current conda(4.10) ships the latest version of Python (3.10). Since Iterable is no longer supported by Python 3.10 and creating environment of snakemake 5.4.5 would create the error above. If snakemake version 5.4.5 is the only version you recommend to run uORF-Tools, perhaps mention it in ReadMe.md and suggest creating the snakemake environment with Python3.7: conda create -c conda-forge -c bioconda -n snakemake snakemake==5.4.5 python==3.7.11

Thanks,
Chao-Jen