Interhost variant calling (Data_Tam_DNAseq_2026_19606wt_dAB_dIJ_mito_flu_on_ATCC19606)

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  1. Input data:

     mkdir bacto; cd bacto;
 mkdir raw_data; cd raw_data;

 # ── Fluoxetine Dataset ──
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcef-1/19606△ABfluEcef-1_1.fq.gz flu_dAB_cef_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcef-1/19606△ABfluEcef-1_2.fq.gz flu_dAB_cef_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcipro-2/19606△ABfluEcipro-2_1.fq.gz flu_dAB_cipro_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcipro-2/19606△ABfluEcipro-2_2.fq.gz flu_dAB_cipro_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEdori-2/19606△ABfluEdori-2_1.fq.gz flu_dAB_dori_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEdori-2/19606△ABfluEdori-2_2.fq.gz flu_dAB_dori_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEnitro-3/19606△ABfluEnitro-3_1.fq.gz flu_dAB_nitro_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEnitro-3/19606△ABfluEnitro-3_2.fq.gz flu_dAB_nitro_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpip-1/19606△ABfluEpip-1_1.fq.gz flu_dAB_pip_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpip-1/19606△ABfluEpip-1_2.fq.gz flu_dAB_pip_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpolyB-3/19606△ABfluEpolyB-3_1.fq.gz flu_dAB_polyB_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpolyB-3/19606△ABfluEpolyB-3_2.fq.gz flu_dAB_polyB_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEtet-1/19606△ABfluEtet-1_1.fq.gz flu_dAB_tet_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△ABfluEtet-1/19606△ABfluEtet-1_2.fq.gz flu_dAB_tet_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcef-4/19606△IJfluEcef-4_1.fq.gz flu_dIJ_cef_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcef-4/19606△IJfluEcef-4_2.fq.gz flu_dIJ_cef_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcipro-3/19606△IJfluEcipro-3_1.fq.gz flu_dIJ_cipro_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcipro-3/19606△IJfluEcipro-3_2.fq.gz flu_dIJ_cipro_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEdori-1/19606△IJfluEdori-1_1.fq.gz flu_dIJ_dori_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEdori-1/19606△IJfluEdori-1_2.fq.gz flu_dIJ_dori_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEnitro-3/19606△IJfluEnitro-3_1.fq.gz flu_dIJ_nitro_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEnitro-3/19606△IJfluEnitro-3_2.fq.gz flu_dIJ_nitro_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpip-4/19606△IJfluEpip-4_1.fq.gz flu_dIJ_pip_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpip-4/19606△IJfluEpip-4_2.fq.gz flu_dIJ_pip_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpolyB-4/19606△IJfluEpolyB-4_1.fq.gz flu_dIJ_polyB_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpolyB-4/19606△IJfluEpolyB-4_2.fq.gz flu_dIJ_polyB_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEcef-1/19606wtfluEcef-1_1.fq.gz flu_wt_cef_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEcef-1/19606wtfluEcef-1_2.fq.gz flu_wt_cef_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEcipro-2/19606wtfluEcipro-2_1.fq.gz flu_wt_cipro_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEcipro-2/19606wtfluEcipro-2_2.fq.gz flu_wt_cipro_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEdori-1/19606wtfluEdori-1_1.fq.gz flu_wt_dori_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEdori-1/19606wtfluEdori-1_2.fq.gz flu_wt_dori_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEnitro-1/19606wtfluEnitro-1_1.fq.gz flu_wt_nitro_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEnitro-1/19606wtfluEnitro-1_2.fq.gz flu_wt_nitro_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEpip-4/19606wtfluEpip-4_1.fq.gz flu_wt_pip_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEpip-4/19606wtfluEpip-4_2.fq.gz flu_wt_pip_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEpolyB-4/19606wtfluEpolyB-4_1.fq.gz flu_wt_polyB_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEpolyB-4/19606wtfluEpolyB-4_2.fq.gz flu_wt_polyB_R2.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEtet-2/19606wtfluEtet-2_1.fq.gz flu_wt_tet_R1.fastq.gz
 ln -s ../../X101SC25116512-Z01-J003/01.RawData/19606wtfluEtet-2/19606wtfluEtet-2_2.fq.gz flu_wt_tet_R2.fastq.gz

 # ── Mitomycin C Dataset ──
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_cipro_1/MitoC_E_AB_cipro_1_1.fq.gz mito_dAB_cipro_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_cipro_1/MitoC_E_AB_cipro_1_2.fq.gz mito_dAB_cipro_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_dori_1/MitoC_E_AB_dori_1_1.fq.gz mito_dAB_dori_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_dori_1/MitoC_E_AB_dori_1_2.fq.gz mito_dAB_dori_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_nitro_2/MitoC_E_AB_nitro_2_1.fq.gz mito_dAB_nitro_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_nitro_2/MitoC_E_AB_nitro_2_2.fq.gz mito_dAB_nitro_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_tet_2/MitoC_E_AB_tet_2_1.fq.gz mito_dAB_tet_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_tet_2/MitoC_E_AB_tet_2_2.fq.gz mito_dAB_tet_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_trime_4/MitoC_E_AB_trime_4_1.fq.gz mito_dAB_trime_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_AB_trime_4/MitoC_E_AB_trime_4_2.fq.gz mito_dAB_trime_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_cipro_1/MitoC_E_IJ_cipro_1_1.fq.gz mito_dIJ_cipro_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_cipro_1/MitoC_E_IJ_cipro_1_2.fq.gz mito_dIJ_cipro_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_dori_4/MitoC_E_IJ_dori_4_1.fq.gz mito_dIJ_dori_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_dori_4/MitoC_E_IJ_dori_4_2.fq.gz mito_dIJ_dori_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_nitro_2/MitoC_E_IJ_nitro_2_1.fq.gz mito_dIJ_nitro_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_nitro_2/MitoC_E_IJ_nitro_2_2.fq.gz mito_dIJ_nitro_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_polyB_3/MitoC_E_IJ_polyB_3_1.fq.gz mito_dIJ_polyB_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_polyB_3/MitoC_E_IJ_polyB_3_2.fq.gz mito_dIJ_polyB_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_tet_3/MitoC_E_IJ_tet_3_1.fq.gz mito_dIJ_tet_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_tet_3/MitoC_E_IJ_tet_3_2.fq.gz mito_dIJ_tet_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_trime_1/MitoC_E_IJ_trime_1_1.fq.gz mito_dIJ_trime_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_IJ_trime_1/MitoC_E_IJ_trime_1_2.fq.gz mito_dIJ_trime_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_cipro_1/MitoC_E_wt_cipro_1_1.fq.gz mito_wt_cipro_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_cipro_1/MitoC_E_wt_cipro_1_2.fq.gz mito_wt_cipro_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_nitro_1/MitoC_E_wt_nitro_1_1.fq.gz mito_wt_nitro_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_nitro_1/MitoC_E_wt_nitro_1_2.fq.gz mito_wt_nitro_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_polyB_1/MitoC_E_wt_polyB_1_1.fq.gz mito_wt_polyB_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_polyB_1/MitoC_E_wt_polyB_1_2.fq.gz mito_wt_polyB_R2.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_trime_2/MitoC_E_wt_trime_2_1.fq.gz mito_wt_trime_R1.fastq.gz
 ln -s ../../X101SC26025981-Z02-J002/01.RawData/MitoC_E_wt_trime_2/MitoC_E_wt_trime_2_2.fq.gz mito_wt_trime_R2.fastq.gz

  2. Call variant calling using snippy

     ln -s ~/Tools/bacto/db/ .;
 ln -s ~/Tools/bacto/envs/ .;
 ln -s ~/Tools/bacto/local/ .;
 cp ~/Tools/bacto/Snakefile .;
 cp ~/Tools/bacto/bacto-0.1.json .;
 cp ~/Tools/bacto/cluster.json .;

 #download CP059040.gb from GenBank
 #mv ~/Downloads/sequence\(2\).gb db/CP059040.gb

 mamba activate /home/jhuang/miniconda3/envs/bengal3_ac3
 (bengal3_ac3) jhuang@WS-2290C:~/DATA/Data_Tam_DNAseq_2023_A6WT_A10CraA_A12AYE_A1917978$ which snakemake
 /home/jhuang/miniconda3/envs/bengal3_ac3/bin/snakemake
 (bengal3_ac3) jhuang@WS-2290C:~/DATA/Data_Tam_DNAseq_2023_A6WT_A10CraA_A12AYE_A1917978$ snakemake -v
 4.0.0 --> CORRECT!

 #NOTE_1: modify bacto-0.1.json keeping only steps assembly, typing_mlst, possibly pangenome and variants_calling true; setting cpu=20 in all used steps.
     #setting the following in bacto-0.1.json
     "fastqc": false,
     "taxonomic_classifier": false,
     "assembly": true,
     "typing_ariba": false,
     "typing_mlst": true,
     "pangenome": true,
     "variants_calling": true,
     "phylogeny_fasttree": false,
     "phylogeny_raxml": false,
     "recombination": false, (due to gubbins-error set false)

     "prokka": {
       "genus": "Acinetobacter",
       "kingdom": "Bacteria",
       "species": "baumannii",
       "cpu": 10,
       "evalue": "1e-06",
       "other": ""
     },

     "mykrobe": {
       "species": "abaum"
     },

     "reference": "db/CP059040.gb"

 #NOTE_2: needs disk Titisee since the pipeline needs /media/jhuang/Titisee/GAMOLA2/TIGRfam_db/TIGRFAMs_15.0_HMM.LIB
 snakemake --printshellcmds

  3. Summarize all SNPs and Indels from the snippy result directory.

     cp ~/Scripts/summarize_snippy_res_ordered.py .
 # IMPORTANT_ADAPT the array in script should be adapted
 isolates = ["flu_wt_cef", "flu_wt_cipro", "flu_wt_dori", "flu_wt_nitro", "flu_wt_pip", "flu_wt_polyB", "flu_wt_tet",    "flu_dAB_cef", "flu_dAB_cipro", "flu_dAB_dori", "flu_dAB_nitro", "flu_dAB_pip", "flu_dAB_polyB", "flu_dAB_tet",    "flu_dIJ_cef", "flu_dIJ_cipro", "flu_dIJ_dori", "flu_dIJ_nitro", "flu_dIJ_pip", "flu_dIJ_polyB",         "mito_dIJ_trime",    "mito_wt_cipro", "mito_wt_nitro", "mito_wt_polyB", "mito_wt_trime",    "mito_dAB_cipro", "mito_dAB_dori", "mito_dAB_nitro", "mito_dAB_tet", "mito_dAB_trime",    "mito_dIJ_cipro", "mito_dIJ_dori", "mito_dIJ_nitro", "mito_dIJ_polyB", "mito_dIJ_tet"]

 mamba activate plot-numpy1
 python3 ./summarize_snippy_res_ordered.py snippy
 #--> Summary CSV file created successfully at: snippy/summary_snps_indels.csv
 cd snippy
 #REMOVE_the_line? I don't find the sence of the line:    grep -v "None,,,,,,None,None" summary_snps_indels.csv > summary_snps_indels_.csv

  4. Using spandx calling variants (almost the same results to the one from viral-ngs!)

     mamba deactivate
 mamba activate /home/jhuang/miniconda3/envs/spandx

 # PREPARE the inputs for the options ref and database
 mkdir ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/PP810610
 cp PP810610.gb  ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/PP810610/genes.gbk
 vim ~/miniconda3/envs/spandx/share/snpeff-5.1-2/snpEff.config
 /home/jhuang/miniconda3/envs/spandx/bin/snpEff build PP810610    #-d
 ~/Scripts/genbank2fasta.py PP810610.gb
 mv PP810610.gb_converted.fna PP810610.fasta    #rename "NC_001348.1 xxxxx" to "NC_001348" in the fasta-file

 ln -s /home/jhuang/Tools/spandx/ spandx
 (spandx) nextflow run spandx/main.nf --fastq "trimmed/*_P_{1,2}.fastq" --ref CP059040.fasta --annotation --database CP059040 -resume

 # RERUN SNP_matrix.sh due to the error ERROR_CHROMOSOME_NOT_FOUND in the variants annotation, resulting in all impacts are MODIFIER --> IT WORKS!
 cd Outputs/Master_vcf
 conda activate /home/jhuang/miniconda3/envs/spandx
 (spandx) cp -r ../../snippy/Y1/reference . # Eigentlich irgendein directory, all directories contains the same reference.
 (spandx) cp ../../spandx/bin/SNP_matrix.sh ./
 #Note that ${variant_genome_path}=CP059040 in the following command, but it was not used after the following command modification.
 #Adapt "snpEff eff -no-downstream -no-intergenic -ud 100 -formatEff -v ${variant_genome_path} out.vcf > out.annotated.vcf" to
 "/home/jhuang/miniconda3/envs/bengal3_ac3/bin/snpEff eff -no-downstream -no-intergenic -ud 100 -formatEff -c reference/snpeff.config -dataDir . ref out.vcf > out.annotated.vcf" in SNP_matrix.sh
 (spandx) bash SNP_matrix.sh CP059040 .

  5. Calling inter-host variants by merging the results from snippy+spandx

    Cross-Caller SNP/Indel Concordance & Invariant Variant Analyzer; Multi-Isolate Variant Intersection, Annotation Harmonization & Caller Discrepancy Report; Comparative Genomic Variant Profiling: Concordance, Invariance & Allele Mismatch Analysis; VarMatch: Cross-Tool Variant Concordance Pipeline

     mamba activate plot-numpy1
 cd bacto
 cp Outputs/Master_vcf/All_SNPs_indels_annotated.txt .
 cp snippy/summary_snps_indels.csv .

 cp ~/Scripts/process_variants_snippy_alleles_spandx_annotations.py .

 #Configuring
 ISOLATES = [
         "flu_wt_cef", "flu_wt_cipro", "flu_wt_dori", "flu_wt_nitro", "flu_wt_pip", "flu_wt_polyB", "flu_wt_tet",
         "flu_dAB_cef", "flu_dAB_cipro", "flu_dAB_dori", "flu_dAB_nitro", "flu_dAB_pip", "flu_dAB_polyB", "flu_dAB_tet",
         "flu_dIJ_cef", "flu_dIJ_cipro", "flu_dIJ_dori", "flu_dIJ_nitro", "flu_dIJ_pip", "flu_dIJ_polyB",
         "mito_dIJ_trime",
         "mito_wt_cipro", "mito_wt_nitro", "mito_wt_polyB", "mito_wt_trime",
         "mito_dAB_cipro", "mito_dAB_dori", "mito_dAB_nitro", "mito_dAB_tet", "mito_dAB_trime",
         "mito_dIJ_cipro", "mito_dIJ_dori", "mito_dIJ_nitro", "mito_dIJ_polyB", "mito_dIJ_tet"
         ]

 (plot-numpy1) python process_variants_snippy_alleles_spandx_annotations.py

 # mv common_variants_all_snippy_annotated.xlsx common_variants_snippy+spandx_annotated_19606wt_dAB_dIJ_mito_flu.xlsx
 # mv common_variants_invariant_snippy_annotated.xlsx common_invariants_snippy+spandx_annotated_19606wt_dAB_dIJ_mito_flu.xlsx

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