no spikeIn chromosomes found with extention _spikein

[sunta3iouxos]

Hi Katarzyna and everyone else, I can not run the spikeIns strings for Chip-seq, this is a CUT&RUN protocol that has the bacteria cary over that can be used to "normalize the samples". this is the full error:

ChIP-seq -d /mnt/c/AP01/bamSpikes -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --peakCaller Genrich --sampleSheet /mnt/c/AP01/bamSpikes/H3K36me3.tsv --windowSize 500 mm10_gencodeM19_spikes /mnt/c/AP01/bamSpikes/H3K36me3_chip_ty
pe.yaml
Sample sheet found and header is ok!

---- This analysis has been done using snakePipes version 2.7.3 ----
Sample sheet found and header is ok!
SystemExit in line 256 of mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile:
1
  File "mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ChIP-seq/Snakefile", line 22, in <module>
  File "mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile", line 256, in <module>
  File "<frozen _sitebuiltins>", line 26, in __call__

 No spikein genome detected - no spikeIn chromosomes found with extention _spikein .


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

The steps I have followed:

createIndices -o CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes --tools bowtie2 -j 6 --local --genomeURL CUT-RUNTools-2.0/assemblies/GRCm38_gencode_release19/genome_fasta/genome.fa --gtfURL CUT-RUNTools-2.0/assemblies/GRCm38_gencode_release19/annotation/genes.gtf  --spikeinGenomeURL CUT-RUNTools-2.0/assemblies/EB1/Sequence/WholeGenomeFasta/genome.fa --spikeinGtfURL CUT-RUNTools-2.0/assemblies/EB1/Annotation/Genes/genes.gtf  --blacklist CUT-RUNTools-2.0/blacklist/mm10.blacklist_merged.bed  mm10_gencodeM19_spikes
DNA-mapping -i /mnt/c/AP01/ -o /mnt/c/AP01/bamSpikes --local --trim --trimmer fastp --trimmerOptions "--trim_poly_g --trim_poly_x -Q -L --correction" --dedup --mapq 2 -j 8 mm10_gencodeM19_spikes
ChIP-seq -d /mnt/c/AP01/bamSpikes -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --peakCaller Genrich --sampleSheet /mnt/c/AP01/bamSpikes/H3K36me3.tsv --windowSize 500 mm10_gencodeM19_spike /mnt/c/AP01/bamSpikes/H3K36me3_chip_type.yaml

and this is my hybrid genome yalm mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/shared/organisms/mm10_gencodeM19_spikes.yaml

blacklist_bed: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/annotation/blacklist.bed
bowtie2_index: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/BowtieIndex/genome
bwa_index: ''
bwa_mem2_index: ''
bwameth2_index: ''
bwameth_index: ''
extended_coding_regions_gtf: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/annotation/genes.slop.gtf
genes_bed: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/annotation/genes.bed
genes_gtf: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/annotation/genes.gtf
genome_2bit: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/genome_fasta/genome.2bit
genome_dict: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/genome_fasta/genome.dict
genome_fasta: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/genome_fasta/genome.fa
genome_index: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/genome_fasta/genome.fa.fai
genome_size: 2652783500
hisat2_index: ''
ignoreForNormalization: ''
known_splicesites: ''
rmsk_file: ''
spikein_blacklist_bed: ''
spikein_genes_gtf: CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/annotation/spikein_genes.gtf
star_index: ''

indexed genome:

genome.1.bt2  genome.2.bt2  genome.3.bt2  genome.4.bt2  genome.fa  genome.rev.1.bt2  genome.rev.2.bt2