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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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createIndices: error: unrecognized arguments: h38 #908

Closed Ci-TJ closed 1 year ago

Ci-TJ commented 1 year ago

Hi! I try to create indices, but failed. What's the problem. The snakePipes is installed in win10 WSL.

(snakePipes) xy@DESKTOP-ILQK2F5:~$ createIndices -o /home/testforsnake --local --genomeURL /home/h38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz / --gtfURL /home/h38/Homo_sapiens.GRCh38.109.gtf.gz h38
usage: /home/anaconda3/envs/snakePipes/bin/createIndices -o OUTDIR [-h] [-v] [-c CONFIGFILE]
                                                            [--clusterConfigFile CLUSTERCONFIGFILE] [-j INT] [--local]
                                                            [--keepTemp] [--snakemakeOptions SNAKEMAKEOPTIONS] [--DAG]
                                                            [--version] [--emailAddress EMAILADDRESS]
                                                            [--smtpServer SMTPSERVER] [--smtpPort SMTPPORT]
                                                            [--onlySSL] [--emailSender EMAILSENDER]
                                                            [--smtpUsername SMTPUSERNAME]
                                                            [--smtpPassword SMTPPASSWORD] --genomeURL GENOMEURL
                                                            [--gtfURL GTFURL] [--spikeinGenomeURL SPIKEINGENOMEURL]
                                                            [--spikeinGtfURL SPIKEINGTFURL] [--spikeinExt SPIKEINEXT]
                                                            [--tools {all,bowtie2,hisat2,bwa,bwa-mem2,bwameth,bwameth2,star,none} [{all,bowtie2,hisat2,bwa,bwa-mem2,bwameth,bwameth2,star,none} ...]]
                                                            [--effectiveGenomeSize EFFECTIVEGENOMESIZE]
                                                            [--spikeinBlacklist SPIKEINBLACKLIST]
                                                            [--blacklist BLACKLIST]
                                                            [--ignoreForNormalization IGNOREFORNORMALIZATION]
                                                            [--rmskURL RMSKURL] [--userYAML]
                                                            GENOME
/home/anaconda3/envs/snakePipes/bin/createIndices: error: unrecognized arguments: h38
(snakePipes) xy@DESKTOP-ILQK2F5:~$ createIndices -o /home/xy/testforsnake --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz  GRCm38_release93

---- This analysis has been done using snakePipes version 2.7.3 ----
Building DAG of jobs...
Using shell: /bin/bash
Provided cluster nodes: 5
Job stats:
job                           count    min threads    max threads
--------------------------  -------  -------------  -------------
all                               1              1              1
bowtie2Index                      1             10             10
bwaIndex                          1              1              1
bwamem2Index                      1              1              1
bwameth2Index                     1              1              1
bwamethIndex                      1              1              1
computeEffectiveGenomeSize        1              1              1
createGenomeFasta                 1              1              1
downloadGTF                       1              1              1
extendGenicRegions                1              1              1
fastaDict                         1              1              1
fastaIndex                        1              1              1
gtf2BED                           1              1              1
hisat2Index                       1             10             10
make2bit                          1              1              1
makeKnownSpliceSites              1             10             10
starIndex                         1             10             10
total                            17              1             10

Select jobs to execute...

[Sun Jul  2 21:15:21 2023]
rule createGenomeFasta:
    output: /home/xy/testforsnake/genome_fasta/genome.fa
    jobid: 1
    reason: Missing output files: /home/xy/testforsnake/genome_fasta/genome.fa
    resources: mem_mb=1000, disk_mb=1000, tmpdir=<TBD>

/bin/sh: 1: module: not found
/bin/sh: 1: sbatch: not found
Error submitting jobscript (exit code 127):

[Sun Jul  2 21:15:21 2023]
rule downloadGTF:
    output: /home/xy/testforsnake/annotation/genes.gtf
    jobid: 5
    reason: Missing output files: /home/xy/testforsnake/annotation/genes.gtf
    resources: mem_mb=1000, disk_mb=1000, tmpdir=<TBD>

/bin/sh: 1: module: not found
/bin/sh: 1: sbatch: not found
Error submitting jobscript (exit code 127):

Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-07-02T211518.518081.snakemake.log

 !!! ERROR in index creation workflow! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Error: snakemake returned an error code of 1, so processing is incomplete!

Best, Seager

adRn-s commented 1 year ago

snakePipes is meant to be run on a cluster, that's why you get the "module" and "sbatch" not found. Those tools (Modules Package, and Slurm Scheduler) are usually installed by IT departments in research institutions.

Also, yout first command has a slash "/" in the middle, right before the --gtfURL parameter. I think you should remove that character so that the positional GENOME argument (h38) is processed instad by the argument parser code.

Good luck!