Error after running snakemake -s xxx --profile xxx

[yashi99]

Thank you for your reply before. Now I can successfully use snakemake, and I have prepared all input files and softwares required for snakemake. I have made the config.yaml and put it in the folder "${workdir}/atac/". However, when I run snakemake -s ${workdir}/cisDynet_snakemake/atacqc/run_snakemake.py --profile ${workdir}/atac/, I got error as shown below. Could you please give me some advice?

snakemake: error: unrecognized arguments: --workdir=/home/storage_4/Projects/Gerline_database/ATAC-Seq/human/ATAC_integration/atac/ --fasta=/home/data/genome/BWA_RNA_UCSCfa_hg38_index/GCA_000001405.15_GRCh38_full_analysis_set.fna --gff3=/home/data/genome/BWA_RNA_UCSCfa_hg38_index/GCA_000001405.15_GRCh38_genomic.gff --effect_genome_size=2700000000.0 --mapping_quality=30 --extsize=150 --shift=75 --smoothLength=20 --binSize=5 --threads=10 --software={'atacqc': '/home/storage_4/Projects/Gerline_database/ATAC-Seq/human/ATAC_integration/cisDynet_snakemake/atacqc', 'trimmomatic': '/home/systools/anaconda3/envs/upstr/bin/trimmomatic', 'bwa': '/home/systools/anaconda3/envs/upstr/bin/bwa', 'bedtools': '/home/systools/anaconda3/envs/upstr/bin/bedtools', 'samtools': '/home/systools/anaconda3/envs/upstr/bin/samtools', 'macs2': '/home/systools/anaconda3/envs/upstr/bin/macs2', 'bamCoverage': '/home/systools/anaconda3/envs/upstr/bin/bamCoverage', 'fadix': '/home/systools/anaconda3/envs/upstr/bin/samtools faidx', 'multiqc': '/home/systools/anaconda3/envs/upstr/bin/multiqc', 'TOBIAS': '/home/systools/anaconda3/envs/tobias/bin/TOBIAS'}

[tzhu-bio]

Please run with snakemake -s cisDynet_snakemake.py -j 20. NOT the snakemake -s run_snakemake.py -j 20.

[yashi99]

Thank you! It works. But it comes to another error:

SyntaxError:
Input and output files have to be specified as strings or lists of strings.
  File "/home/storage_4/Projects/Gerline_database/ATAC-Seq/human/ATAC_integration/cisDynet_snakemake/atacqc/cisDynet_snakemake.py", line 449, in <module>

it may because I did not give input files for motif: , adapters: , and organell_chr: ? Or some other causes? If it is, I wonder how can I prepare those files?

[tzhu-bio]

motif can be downloaded from https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_non-redundant_pfms_meme.txt. _organellchr can be filled with hg19 or hg38 mitochondrial chromosome number, like "ChrM". adapters can be found in the directory of your installed trimmomatic software. Please refer to the path in the config I provided you to find it.

[yashi99]

That works! Thank you!