RuleException in rule validateFQ: The name 'snakePipes_cluster_logDir' is unknown in this context

[sunta3iouxos]

Hi all and happy new year. Wishing for the best and a continuing development of the snakepipes.

I installed the latest snakeppes to do some mapping and I got an error:

RuleException in rule validateFQ in file /scratch/tgeorgom/mamba/snakePipesTest/lib/python3.12/site-packages/snakePipes/shared/rules/FASTQ.snakefile, line 2:
NameError: The name 'snakePipes_cluster_logDir' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}}, when formatting the following:
mkdir -p logs/{rule}; sbatch --nodes 1 -p smp-rh7 -A tgeorgom -c {threads} -e {snakePipes_cluster_logDir}/{rule}.%j.err --mem-per-cpu={resources.mem} --job-name=snakePipes_{rule}-{wildcards} --output=logs/{rule}/{rule}-{wildcards}-%j.out --time={resources.time} --parsable

This is the compete output:

verbose: True
workingdir: /scratch/tgeorgom/24D309_mm39
--------------------------------------------------------------------------------


--- Genome ---------------------------------------------------------------------
config file: /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/mm39_gencodevM34.yaml
blacklist_bed: /home/tgeorgom/assemblies/mm39/annotation/blacklist.bed
bowtie2_index:
bwa_index: /home/tgeorgom/assemblies/mm39/BWAIndex/genome
bwa_mem2_index:
bwameth2_index:
bwameth_index:
extended_coding_regions_gtf: /home/tgeorgom/assemblies/mm39/annotation/genes.slop.gtf
genes_bed: /home/tgeorgom/assemblies/mm39/annotation/genes.bed
genes_gtf: /home/tgeorgom/assemblies/mm39/annotation/genes.gtf
genome_2bit: /home/tgeorgom/assemblies/mm39/genome_fasta/genome.2bit
genome_fasta: /home/tgeorgom/assemblies/mm39/genome_fasta/genome.fa
genome_index: /home/tgeorgom/assemblies/mm39/genome_fasta/genome.fa.fai
genome_size: 2654621783
hisat2_index:
ignoreForNormalization: MT X Y JH584299.1 GL456233.2 JH584301.1 GL456211.1 GL456221.1 JH584297.1 JH584296.1 GL456354.1 JH584298.1 JH584300.1 GL456219.1 GL456210.1 JH584303.1 JH584302.1 GL456212.1 JH584304.1 GL456379.1 GL456366.1 GL456367.1 GL456239.1 GL456383.1 GL456385.1 GL456360.1 GL456378.1 MU069435.1 GL456389.1 GL456372.1 GL456370.1 GL456381.1 GL456387.1 GL456390.1 GL456394.1 GL456392.1 GL456382.1 GL456359.1 GL456396.1 GL456368.1 MU069434.1 JH584295.1 chr1_GL456210v1_random chr1_GL456211v1_random chr1_GL456212v1_random chr1_GL456221v1_random chr1_MU069434v1_random chr1_GL456239v1_random chr4_JH584295v1_random chr5_JH584296v1_random chr5_JH584297v1_random chr5_JH584298v1_random chr5_GL456354v1_random chr5_JH584299v1_random chr7_GL456219v1_random chrM chrUn_GL456359v1 chrUn_GL456360v1 chrUn_GL456366v1 chrUn_GL456367v1 chrUn_GL456368v1 chrUn_GL456370v1 chrUn_GL456372v1 chrUn_GL456378v1 chrUn_GL456379v1 chrUn_GL456381v1 chrUn_GL456382v1 chrUn_GL456383v1 chrUn_GL456385v1 chrUn_GL456387v1 chrUn_GL456389v1 chrUn_GL456390v1 chrUn_GL456392v1 chrUn_GL456394v1 chrUn_GL456396v1 chrUn_JH584304v1 chrUn_MU069435v1 chrX_GL456233v2_random chrY_JH584300v1_random chrY_JH584301v1_random chrY_JH584302v1_random chrY_JH584303v1_random
known_splicesites:
rmsk_file:
star_index:
--------------------------------------------------------------------------------

--- Workflow parameters --------------------------------------------------------
samples: ['A006850396_234176_S1', 'A006850396_234179_S2', 'A006850396_234181_S27', 'A006850396_234184_S28', 'A006850396_234187_S29', 'A006850396_234189_S30', 'A006850396_234191_S31', 'A006850396_234193_S32', 'A006850396_234195_S33', 'A006850396_234197_S34', 'A006850396_234199_S35', 'A006850396_234201_S36', 'A006850396_234204_S37', 'A006850396_234206_S38', 'A006850396_234208_S39', 'A006850396_234210_S40', 'A006850396_234212_S41', 'A006850396_234214_S42', 'A006850396_234216_S43', 'A006850396_234218_S44', 'A006850396_234220_S45', 'A006850396_234222_S46', 'A006850396_234224_S47', 'A006850396_234226_S48', 'A006850396_234228_S49', 'A006850396_234230_S50', 'A006850396_234232_S3', 'A006850396_234234_S51', 'A006850396_234236_S4']
paired: True
read extension: ['_L000_R1_001', '_L000_R2_001']
fastq dir: FASTQ_fastp
maximum insert size (Bowtie2 -X): 5000

some more information on my setup:

------------------------- Info -------------------------

The global configuration file is:
    /scratch/tgeorgom/mamba/snakePipesTest/lib/python3.12/site-packages/snakePipes/shared/defaults.yaml
    --> tempDir in the global configuration = /scratch/tgeorgom/temp
    --> The snakemake profile used =  /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/profiles/snakepipes_genericprofile

Organism YAML files:
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/SchizoSPombe_ASM294v2.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/mm39_gencodevM34.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/GRCz10.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/mm10_gencodeM19.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/GRCh38_gencode40.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/GRCz11.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/mm39_ens106.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/hg38.yaml
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/organisms/dm6.yaml
(/scratch/tgeorgom/mamba/snakePipesTest) [tgeorgom@cheops1:~]$ 09:21:13$snakePipes version

snakepipes version

snakePipes version 3.0.0

and my environment":

envs/shared.yaml: /scratch/tgeorgom/mamba/snakePipes/env/4be21c97c6dbd6d46289cfde95cd28d3
envs/createIndices.yaml: /scratch/tgeorgom/mamba/snakePipes/env/cd368591412a52e6d5d07c302c75b990
envs/rna_seq.yaml: /scratch/tgeorgom/mamba/snakePipes/env/7b098b94bad80d0be19669458b1d7ef9
envs/salmon.yaml: /scratch/tgeorgom/mamba/snakePipes/env/91c0862e669c863faaafacb43e0698fa
envs/sleuth.yaml: /scratch/tgeorgom/mamba/snakePipes/env/d2328ce9b4f1ceca176085bd7efa9983
envs/rMats.yaml: /scratch/tgeorgom/mamba/snakePipes/env/e33a1a10649f4265cf4ff2baba590d6b
envs/sc_rna_seq.yaml: /scratch/tgeorgom/mamba/snakePipes/env/230aa974c6a017b0bdbe1ee88bb3c22c
envs/sc_rna_seq_seurat.yaml: /scratch/tgeorgom/mamba/snakePipes/env/6722693fd6eae6bf2573c001a98e9ee0
envs/sc_rna_seq_loompy.yaml: /scratch/tgeorgom/mamba/snakePipes/env/eb6a61a9ffe2bbf9a9d93ab36a482653
envs/sc_rna_seq_alevinqc.yaml: /scratch/tgeorgom/mamba/snakePipes/env/11de9242b49c636bcb0ec64af69885ef
envs/sc_rna_seq_eisaR.yaml: /scratch/tgeorgom/mamba/snakePipes/env/c40434e729db26f236c3fa1dce9c0218
envs/dna_mapping.yaml: /scratch/tgeorgom/mamba/snakePipes/env/7a63632da50020395ff9db233e3231d9
envs/chip_seq.yaml: /scratch/tgeorgom/mamba/snakePipes/env/c75edc1f1e76e959255cc668cd52f0dd
envs/atac_seq.yaml: /scratch/tgeorgom/mamba/snakePipes/env/62bcdbbfa4341f35f613e3332bbe781b
envs/hic.yaml: /scratch/tgeorgom/mamba/snakePipes/env/248314a652784ded5237ea91c9d4bd35
envs/makePairs.yaml: /scratch/tgeorgom/mamba/snakePipes/env/ab9e3de32b1bd1d3f5a4311c6aaed24c
envs/wgbs.yaml: /scratch/tgeorgom/mamba/snakePipes/env/ca3f9b13c24ceebd3aac870cc359ae90
envs/wgbs_dss.yaml: /scratch/tgeorgom/mamba/snakePipes/env/632893ec37fc0387df70304d8778bc69
envs/rmarkdown.yaml: /scratch/tgeorgom/mamba/snakePipes/env/2562d529b75780fec98b5eb12583a945
envs/preprocessing.yaml: /scratch/tgeorgom/mamba/snakePipes/env/fec6e7304c8e6327a5a04faeffd83796
envs/noncoding.yaml: /scratch/tgeorgom/mamba/snakePipes/env/daab59214d43e974341a138c904f2395
envs/sambamba.yaml: /scratch/tgeorgom/mamba/snakePipes/env/49eb0582715a9969a4e1a76c0857647b
envs/pysam.yaml: /scratch/tgeorgom/mamba/snakePipes/env/f71b1e29fc7b83c4e7d4959924ec5f54
envs/chip_seacr.yaml: /scratch/tgeorgom/mamba/snakePipes/env/91f30208e342051a57c40c2b11acb8b2

[katsikora]

Hi,

thanks for reporting the issue. @WardDeb , could you kindly take a look?

Best wishes,

Katarzyna

[WardDeb]

Can you share the content of
/scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/profiles/snakepipes_genericprofile/config.yaml

More specifically, all the lines above 'set-resources'
Aside from this, note that 3.0.0 will fail due to the fq problem (cfr. #1075), probably best to move to 3.1.0 if you are still setting up.