Typing of S. epidermidis samples (HDMx samples)

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Tags: processing

SCCmec_HDMs

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786320/

Classification of Staphylococcal Cassette Chromosome mec (SCCmec): Guidelines for Reporting Novel SCCmec Elements

mec gene complex.

IS1272 is part of the IS1182 family of insertion sequences

  • The mec gene complex is composed of mecA, its regulatory genes, and associated insertion sequences.
  • The class A mec gene complex (class A mec) is the prototype complex, which contains mecA, the complete mecR1 and mecI regulatory genes upstream of mecA, and the hypervariable region (HVR) and insertion sequence IS431 downstream of mecA.
    • The class B mec gene complex is composed of mecA, a truncated mecR1 resulting from the insertion of IS1272 upstream of mecA, and [HVR and IS431 downstream of mecA].
  • The class C mec gene complex contains mecA and truncated mecR1 by the insertion of IS431 upstream of mecA and HVR and IS431 downstream of mecA.
  • There are two distinct class C mec gene complexes; in the class C1 mec gene complex, the IS431 upstream of mecA has the same orientation as the IS431 downstream of mecA (next to HVR), while in the class C2 mec gene complex, the orientation of IS431 upstream of mecA is reversed.
  • C1 and C2 are regarded as different mec gene complexes since they have likely evolved independently.
  • The class D mec gene complex is composed of mecA and ΔmecR1 but does not carry an insertion sequence downstream of ΔmecR1 (as determined by PCR analysis).

  • Several variants within the major classes of the mec gene complex have been described, including insertions of IS431 or IS1182 upstream of mecA in the class A mec gene complex or insertion of Tn4001 upstream of mecA in the class B mec complex.

  • run with bengal3

    1. cd ~/DATA/Data_Denise_CalCov1
    2. cp bacto-0.1.json ../Data_Denise_CalCov2
    3. cp cluster.json ../Data_Denise_CalCov2
    4. cp Snakefile ../Data_Denise_CalCov2
    5. ln -s /home/jhuang/Tools/bacto/local .
    6. ln -s /home/jhuang/Tools/bacto/db .
    7. ln -s /home/jhuang/Tools/bacto/envs .
    8. mkdir raw_data; cd raw_data
    9. ln -s ../Alignment_Imported_1/20240913_174420/Fastq/HDM7_S1_L001_R1_001.fastq.gz HDM7_R1.fastq.gz
    10. ln -s ../Alignment_Imported_1/20240913_174420/Fastq/HDM7_S1_L001_R2_001.fastq.gz HDM7_R2.fastq.gz
    11. ln -s ../Alignment_Imported_1/20240913_174420/Fastq/HDM10_S2_L001_R1_001.fastq.gz HDM10_R1.fastq.gz
    12. ln -s ../Alignment_Imported_1/20240913_174420/Fastq/HDM10_S2_L001_R2_001.fastq.gz HDM10_R2.fastq.gz
    14. ln -s ../20240812_FS10003086_50_BSB09416-2831/Alignment_Imported_1/20240813_202730/Fastq/HDM1_S1_L001_R1_001.fastq.gz HDM1_R1.fastq.gz
    15. ln -s ../20240812_FS10003086_50_BSB09416-2831/Alignment_Imported_1/20240813_202730/Fastq/HDM1_S1_L001_R2_001.fastq.gz HDM1_R2.fastq.gz
    16. ln -s ../20240913/Alignment_Imported_1/20240913_174420/Fastq/HDM7_S1_L001_R1_001.fastq.gz HDM7_R1.fastq.gz
    17. ln -s ../20240913/Alignment_Imported_1/20240913_174420/Fastq/HDM7_S1_L001_R2_001.fastq.gz HDM7_R2.fastq.gz
    18. ln -s ../20240913/Alignment_Imported_1/20240913_174420/Fastq/HDM10_S2_L001_R1_001.fastq.gz HDM10_R1.fastq.gz
    19. ln -s ../20240913/Alignment_Imported_1/20240913_174420/Fastq/HDM10_S2_L001_R2_001.fastq.gz HDM10_R2.fastq.gz
    20. ln -s ../20240919_FS10003086_61_BSB09416-2735/Alignment_Imported_1/20240920_173408/Fastq/HDM11-SF1_S1_L001_R1_001.fastq.gz HDM11-SF1_R1.fastq.gz
    21. ln -s ../20240919_FS10003086_61_BSB09416-2735/Alignment_Imported_1/20240920_173408/Fastq/HDM11-SF1_S1_L001_R2_001.fastq.gz HDM11-SF1_R2.fastq.gz
    22. ln -s ../20240919_FS10003086_61_BSB09416-2735/Alignment_Imported_1/20240920_173408/Fastq/HDM15-SF2_S2_L001_R1_001.fastq.gz HDM15-SF2_R1.fastq.gz
    23. ln -s ../20240919_FS10003086_61_BSB09416-2735/Alignment_Imported_1/20240920_173408/Fastq/HDM15-SF2_S2_L001_R2_001.fastq.gz HDM15-SF2_R2.fastq.gz
    25. # only activate the steps assembly and mlst in bacto-0.1.json.
    26. (bengal3_ac3) jhuang@WS-2290C:~/Documents$ /home/jhuang/miniconda3/envs/snakemake_4_3_1/bin/snakemake --printshellcmds
    28. # -- Results --
    29. shovill/HDM1/contigs.fa sepidermidis    5       arcC(1) aroE(1) gtr(1)  mutS(2) pyrR(2) tpiA(1) yqiL(1)
    30. HDM10.mlst.txt:shovill/HDM10/contigs.fa sepidermidis    59      arcC(2) aroE(1) gtr(1)  mutS(1) pyrR(2) tpiA(1) yqiL(1)
    31. HDM7.mlst.txt:shovill/HDM7/contigs.fa   sepidermidis    59      arcC(2) aroE(1) gtr(1)  mutS(1) pyrR(2) tpiA(1) yqiL(1)

  • run with bakta

    1. #under env (bakta)
    2. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    3.     bakta --db /mnt/nvme0n1p1/bakta_db shovill/${sample}/contigs.fa --prefix ${sample}
    4. done

  • mapping on assembly to calculate the coverage

    1. #samtools depth input.bam > depth.txt
    2. #samtools depth input.bam | awk '{sum+=$3} END { print "Average coverage:",sum/NR}'
    3. #bedtools coverage -a regions.bed -b input.bam > coverage.txt
    4. #bedtools coverage -a regions.bed -b input.bam -d > coverage_per_base.txt
    6. bwa index ./shovill/HDM1/contigs.fa
    7. bwa mem ./shovill/HDM1/contigs.fa fastq/HDM1_1.fastq fastq/HDM1_2.fastq > aligned.sam
    8. samtools view -Sb aligned.sam > aligned.bam
    9. samtools sort aligned.bam -o sorted.bam
    10. samtools index sorted.bam
    11. samtools depth sorted.bam > depth.txt
    12. awk '{sum+=$3} END { print "Average coverage:",sum/NR}' depth.txt
    13. bedtools coverage -a regions.bed -b sorted.bam > coverage.txt
    14. bedtools genomecov -ibam sorted.bam -d > coverage_per_base.txt
    16. # Step 1: Calculate depth using samtools
    17. samtools depth sorted.bam > depth.txt
    18. # Step 2: Calculate average depth using awk
    19. awk '{sum+=$3; count++} END {print "Average Coverage:", sum/count}' depth.txt
    21. # Step 1: Calculate coverage with bedtools for a BED file
    22. #bedtools coverage -a regions.bed -b input.bam > coverage.txt
    23. # Step 2: Process the output with awk
    24. #awk '{ sum+=$7 } END { print "Average coverage depth:", sum/NR }' coverage.txt
    26. bwa index ./shovill/HDM7/contigs.fa
    27. bwa mem ./shovill/HDM7/contigs.fa fastq/HDM7_1.fastq fastq/HDM7_2.fastq > aligned_HDM7.sam
    28. samtools view -Sb aligned_HDM7.sam > aligned_HDM7.bam
    29. samtools sort aligned_HDM7.bam -o sorted_HDM7.bam
    30. samtools index sorted_HDM7.bam
    31. # Step 1: Calculate depth using samtools
    32. samtools depth sorted_HDM7.bam > depth_HDM7.txt
    33. # Step 2: Calculate average depth using awk
    34. awk '{sum+=$3; count++} END {print "Average Coverage:", sum/count}' depth_HDM7.txt
    35. #Average Coverage: 380.079
    37. bwa index ./shovill/HDM10/contigs.fa
    38. bwa mem ./shovill/HDM10/contigs.fa fastq/HDM10_1.fastq fastq/HDM10_2.fastq > aligned_HDM10.sam
    39. samtools view -Sb aligned_HDM10.sam > aligned_HDM10.bam
    40. samtools sort aligned_HDM10.bam -o sorted_HDM10.bam
    41. samtools index sorted_HDM10.bam
    42. # Step 1: Calculate depth using samtools
    43. samtools depth sorted_HDM10.bam > depth_HDM10.txt
    44. # Step 2: Calculate average depth using awk
    45. awk '{sum+=$3; count++} END {print "Average Coverage:", sum/count}' depth_HDM10.txt
    46. #Average Coverage: 254.704

  • SCCmec typing and drawing with clinker

    1. #1. -- HDM1_contigs.fa --
    3. One SCCmec element detected.
    5. Prediction based on genes:
    6. Predicted SCCmec element: SCCmec_type_IV(2B)
    8. Prediction based on homology to whole cassette:
    9. Predicted whole cassette and %template coverage: SCCmec_type_IV(2B) 79.92%
    11. Predicted genes:
    12. Fasta header % Identity Query/HSP Length Contig Position in contig
    14. ccrA2:7:81108:AB096217  100.00  1350/1350   contig00032 3770..5119
    15. ccrB2:9:JCSC4469:AB097677   99.94   1650/1650   contig00032 5120..6769
    16. IS1272:3:AM292304   99.95   1844/1843   contig00032 8611..10454
    17. dmecR1:1:AB033763   100.00  987/987 contig00032 10443..11429
    18. mecA:12:AB505628    100.00  2010/2010   contig00032 11526..13535
    20. samtools faidx shovill/HDM1_contigs.fa
    21. samtools faidx shovill/HDM1_contigs.fa contig00032:1-13635 > HDM1_sub.fna
    22. bakta --db /mnt/nvme0n1p1/bakta_db HDM1_sub.fna
    24. #2. -- HDM7_contigs.fa --
    26. One SCCmec element detected.
    28. Prediction based on genes:
    29. Predicted SCCmec element: SCCmec_type_IVa(2B)
    31. Prediction based on homology to whole cassette:
    32. Predicted whole cassette and %template coverage: SCCmec_type_IVa(2B) 84.24%
    34. Predicted genes:
    35. Fasta header % Identity Query/HSP Length Contig Position in contig
    37. mecA:12:AB505628    100.00  2010/2010   contig00014 2800..4809
    38. dmecR1:1:AB033763   99.90   987/987 contig00014 4906..5892
    39. IS1272:3:AM292304   100.00  1843/1843   contig00014 5881..7723
    40. ccrB2:3:CA05:AB063172   100.00  1629/1629   contig00014 9565..11193
    41. ccrA2:3:CA05:AB063172   100.00  1350/1350   contig00014 11215..12564
    42. subtype-IVa(2B):1:CA05:AB063172 100.00  1491/1491   contig00014 16461..17951
    43. #IS1272:2:AB033763  91.06   1577/1585   contig00001 369260..370836
    45. samtools faidx shovill/HDM7_contigs.fa
    46. samtools faidx shovill/HDM7_contigs.fa contig00014:2700-18051 > HDM7_sub.fna
    47. bakta --db /mnt/nvme0n1p1/bakta_db HDM7_sub.fna
    49. mecA
    50. dmecR1
    51. Type I restriction enzyme HindI endonuclease subunit-like C-terminal domain-containing protein
    52. IS1272
    53. DUF1643 domain-containing protein
    54. Pyridoxal phosphate-dependent enzyme
    55. hypothetical protein
    56. ccrB2
    57. ccrA2
    58. DUF927 domain-containing protein
    59. hypothetical protein
    60. ACP synthase
    61. AAA family ATPase (= subtype-IVa(2B))
    63. #3. -- HDM10_contigs.fa --
    65. Prediction based on genes:
    66. Predicted SCCmec element: SCCmec_type_IV(2B&5)
    68. Prediction based on homology to whole cassette:
    69. Predicted whole cassette and % template coverage: SCCmec_type_IV(2B) 84.37%
    71. Predicted genes:
    73. Fasta header % Identity Query/HSP Length Contig Position in contig
    75. subtype-IVa(2B):1:CA05:AB063172 100.00  1491/1491   contig00020 4152..5642
    76. ccrA2:3:CA05:AB063172   100.00  1350/1350   contig00020 9539..10888
    77. ccrB2:3:CA05:AB063172   100.00  1629/1629   contig00020 10910..12538
    78. IS1272:3:AM292304   100.00  1843/1843   contig00020 14380..16222
    79. dmecR1:1:AB033763   100.00  987/987 contig00020 16211..17197
    80. mecA:12:AB505628    100.00  2010/2010   contig00020 17294..19303
    81. #IS1272:2:AB033763  90.75   1579/1585   contig00033 2..1580
    82. #ccrC1-allele-2:1:AB512767  90.95   1680/1680   contig00022 9836..11515
    84. samtools faidx shovill/HDM10_contigs.fa
    85. samtools faidx shovill/HDM10_contigs.fa contig00020:4052-19403 > HDM10_sub.fna
    86. bakta --db /mnt/nvme0n1p1/bakta_db HDM10_sub.fna
    88. #4. -- HDM11-SF1_contigs.fa --
    90. No SCCmec element was detected
    92. Prediction based on genes:
    93. Predicted SCCmec element: none
    95. Prediction based on homology to whole cassette:
    96. Predicted whole cassette and %template coverage: none
    98. #5. -- HDM15-SF2_contigs.fa --
    100. SCCmec_type_IV(2B)
    101. SCCmec_type_VI(4B)
    102. Following gene complexes based on prediction of genes was detected :
    103. ccr class 2
    104. ccr class 4
    105. mec class B
    107. Predicted genes:
    108. Fasta header % Identity Query/HSP Length Contig Position in contig
    110. ccrA2:7:81108:AB096217  100.00  1350/1350   contig00004 3823..5172
    111. ccrB2:9:JCSC4469:AB097677   99.94   1650/1650   contig00004 5173..6822
    112. IS1272:3:AM292304   99.95   1844/1843   contig00004 8664..10507
    113. dmecR1:1:AB033763   100.00  987/987 contig00004 10496..11482
    114. mecA:12:AB505628    100.00  2010/2010   contig00004 11579..13588
    116. subtyppe-Vc(5C2&5):10:AB505629  99.84   1935/1935   contig00004 20148..22082
    118. ccrA4:2:BK20781:FJ670542    90.53   1362/1362   contig00004 24570..25931
    119. ccrB4:2:BK20781:FJ670542    91.68   1635/1629   contig00004 25928..27562
    121. subtype-IVa(2B):1:CA05:AB063172 100.00  1491/1491   contig00015 52228..53718
    123. samtools faidx shovill/HDM7_contigs.fa
    124. samtools faidx shovill/HDM7_contigs.fa contig00014:2700-18051 > HDM7_sub.fna
    125. bakta --db /mnt/nvme0n1p1/bakta_db HDM7_sub.fna
    127. samtools faidx shovill/HDM10_contigs.fa
    128. samtools faidx shovill/HDM10_contigs.fa contig00020:4052-19403 > HDM10_sub.fna
    129. bakta --db /mnt/nvme0n1p1/bakta_db HDM10_sub.fna
    131. samtools faidx shovill/HDM15-SF2_contigs.fa
    132. samtools faidx shovill/HDM15-SF2_contigs.fa contig00004:1-27662 > HDM15-SF2_sub.fna
    133. samtools faidx shovill/HDM15-SF2_contigs.fa contig00015:52128-53818 >> HDM15-SF2_sub.fna
    134. bakta --db /mnt/nvme0n1p1/bakta_db HDM15-SF2_sub.fna
    136. #END
    137. #172.104.140.19
    139. mkdir gbff_sub
    140. mv *_sub.gbff gbff_sub
    141. cd gbff_sub
    142. for f in *_sub.gbff; do mv "$f" "${f/_sub.gbff/.gbff}"; done
    143. #mv HDM1_sub.gbff HDM1.gbff
    144. #mv HDM7_sub.gbff HDM7.gbff
    145. #mv HDM10_sub.gbff HDM10.gbff
    146. #mv HDM15-SF2_sub.gbff HDM15-SF2.gbff
    148. rm *.json
    149. clinker *.gbff -p plot_HDRNA.html --dont_set_origin -s session_HDRNA.json -o alignments_HDRNA.csv -dl "," -dc 4
    151. cp ./gbff_HDRNA_01/clinker.png HDRNA_01_clinker.png

  • Arg typing

    1. grep "agrD" *.gbff | sort
    3. HDM1.gbff:                     /gene="agrD"
    4. HDM1.gbff:                     /gene="agrD"
    5. HDM7.gbff:                     /gene="agrD"
    6. HDM7.gbff:                     /gene="agrD"
    7. HDM10.gbff:                     /gene="agrD"
    8. HDM10.gbff:                     /gene="agrD"
    9. HDM11-SF1.gbff:                     /gene="agrD"
    10. HDM11-SF1.gbff:                     /gene="agrD"
    11. HDM15-SF2.gbff:                     /gene="agrD"
    12. HDM15-SF2.gbff:                     /gene="agrD"
    14. MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE
    15. MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE
    16. MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE
    17. MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE
    18. MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE
    20. #* The agr typing is not defined, as I have compared the sequence with the amino acid sequences of ArgD described in the paper available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187671/. It does not correspond to Type I, Type II, or Type III. (For more details, see below).
    22. -- AgrD I --
    23. Query  1       MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE  46
    24.         M  +  L +K F+  +  IG  +  + C  Y DEP+VPEELTKL E
    25. Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
    27. -- AgrD II --
    28. Query  1       MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE  46
    29.         MNLLGGLLLKIFSNFMAVIGNASKYNPC  YLDEPQVPEELTKLDE
    30. Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
    32. -- AgrD III --
    33. Query  1       MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE  46
    34.         MNLLGGLLLK+FSNFMAVIGNA+KYNPC  YLDEPQVPEELTKLDE
    35. Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688

  • calulate the presence-absence-matrix for predefined gene list

    1. #start codon: ATG, GTG und TTG
    2. #stop codon: 5'-UAA-3', 5'-UGA-3' und 5'-UAG-3' --> TAA, TGA, TAG
    4. ./Staphylococcus_aureus_MRSA252.fasta
    5. ./Staphylococcus_epidermidis_RP62A.fasta
    6. ./Enterococcus_faecium_isolate_E300_pathogenicity_island.fasta
    8. # -- Hause keeper: gyrB --
    9. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":2609812-2611743 > gyrB.fasta
    10. #revcomp gyrB.fasta > gyrB_revcomp.fasta
    11. gyrB_revcomp.fasta
    13. # -- Metabolic genes: fumC, gltA, icd --
    14. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":1444326-1445711 > fumC.fasta
    15. #revcomp fumC.fasta > fumC_revcomp.fasta
    16. ./fumC_revcomp.fasta
    17. ./gltA.fasta
    18. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":1296195-1297463 > icd.fasta
    19. #revcomp icd.fasta > icd_revcomp.fasta
    20. icd_revcomp.fasta
    22. # -- Virulence regulartors: apsS, sigB, sarA, agrC, yycG --
    23. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":316151-317191 > apsS.fasta
    24. apsS.fasta
    25. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":1722805-1723575 > sigB.fasta
    26. #revcomp sigB.fasta > sigB_revcomp.fasta
    27. sigB_revcomp.fasta
    28. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":279424-279798 > sarA.fasta
    29. #revcomp sarA.fasta > sarA_revcomp.fasta
    30. sarA_revcomp.fasta
    31. ./agrC.fasta
    32. ./yycG.fasta
    34. # -- Toxins: psmβ1, hlb --
    35. ./psm-beta.fasta
    36. #psm-beta1.fasta
    37. ./hlb_.fasta
    38. #./hlb.fasta
    40. # -- Biofilm formation: atlE, sdrG, sdrH, ebh, ebp, tagB --
    41. ./atlE.fasta
    42. ./sdrG.fasta
    44. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":1555024-1556469 > sdrH.fasta
    45. #revcomp sdrH.fasta > sdrH_revcomp.fasta
    46. sdrH_revcomp.fasta
    48. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":1023531-1053980 > ebh.fasta
    49. #revcomp ebh.fasta > ebh_revcomp.fasta
    50. ebh_revcomp.fasta
    52. #https://www.ncbi.nlm.nih.gov/gene/?term=(Elastin-binding+protein)+AND+%22Staphylococcus+aureus%22%5Bporgn%3A__txid1282%5D
    53. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":1094204-1095586 > ebpS.fasta
    54. #revcomp ebpS.fasta > ebpS_revcomp.fasta
    55. ebpS_revcomp.fasta
    56. ./tagB.fasta
    58. # -- Immune evasion & colonization: capC, sepA, dltA, fmtC, lipA, sceD, SE0760 --
    60. ./capC.fasta
    61. #./capBCA_ywtC.fasta
    62. ./sepA.fasta
    63. #./ORF123_sepA_ORF5.fasta
    65. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":503173-504630 > dltA.fasta
    66. dltA.fasta
    67. ./fmtC.fasta
    68. #samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":498445-499359 > lipA.fasta
    69. lipA.fasta
    70. ./sceD.fasta
    71. #./sceDAE.fasta
    72. ./SE0760.fasta
    74. # -- Serine protease: esp, ecpA --
    75. ./esp.fasta
    76. ./ecpA_.fasta
    77. #./ecpA.fasta
    79. # -- Phage: PhiSepi-HH1, PI-Sepi-HH2, PhiSepi-HH3 (#HH1-HP1, HH3-HP2, HH3-TreR) --
    80. ./MT880870.fasta
    81. ./MT880871.fasta
    82. ./MT880872.fasta
    84. #Note that write a message to Holger, say "ebp gene does not exist, instead of it only ebpS gene exists!"
    86. makeblastdb -in HDM1_contigs.fa -dbtype nucl
    87. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    88.   blastn -db ../shovill/${sample}_contigs.fa -query gyrB_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gyrB_on_${sample}.blastn
    89. done
    91. ./fumC_revcomp.fasta
    92. ./gltA.fasta
    93. icd_revcomp.fasta
    95. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    96.   blastn -db ../shovill/${sample}_contigs.fa -query fumC_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fumC_on_${sample}.blastn
    97. done
    98. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    99.   blastn -db ../shovill/${sample}_contigs.fa -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_${sample}.blastn
    100. done
    101. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    102.   blastn -db ../shovill/${sample}_contigs.fa -query icd_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > icd_on_${sample}.blastn
    103. done
    105. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    106.   blastn -db ../shovill/${sample}_contigs.fa -query apsS.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > apsS_on_${sample}.blastn
    107. done
    108. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    109.   blastn -db ../shovill/${sample}_contigs.fa -query sigB_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sigB_on_${sample}.blastn
    110. done
    111. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    112.   blastn -db ../shovill/${sample}_contigs.fa -query sarA_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sarA_on_${sample}.blastn
    113. done
    114. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    115.   blastn -db ../shovill/${sample}_contigs.fa -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_${sample}.blastn
    116. done
    117. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    118.   blastn -db ../shovill/${sample}_contigs.fa -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_${sample}.blastn
    119. done
    121. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    122.   blastn -db ../shovill/${sample}_contigs.fa -query psm-beta.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta_on_${sample}.blastn
    123. done
    124. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    125.   blastn -db ../shovill/${sample}_contigs.fa -query psm-beta1.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_${sample}.blastn
    126. done
    127. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    128.   blastn -db ../shovill/${sample}_contigs.fa -query hlb_.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_${sample}.blastn
    129. done
    131. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    132.   blastn -db ../shovill/${sample}_contigs.fa -query atlE.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_${sample}.blastn
    133. done
    134. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    135.   blastn -db ../shovill/${sample}_contigs.fa -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_${sample}.blastn
    136. done
    137. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    138.   blastn -db ../shovill/${sample}_contigs.fa -query sdrH_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrH_on_${sample}.blastn
    139. done
    140. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    141.   blastn -db ../shovill/${sample}_contigs.fa -query ebh_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ebh_on_${sample}.blastn
    142. done
    143. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    144.   blastn -db ../shovill/${sample}_contigs.fa -query ebpS_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ebpS_on_${sample}.blastn
    145. done
    146. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    147.   blastn -db ../shovill/${sample}_contigs.fa -query tagB.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_${sample}.blastn
    148. done
    150. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    151.   blastn -db ../shovill/${sample}_contigs.fa -query capC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_${sample}.blastn
    152. done
    153. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    154.   blastn -db ../shovill/${sample}_contigs.fa -query sepA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_${sample}.blastn
    155. done
    156. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    157.   blastn -db ../shovill/${sample}_contigs.fa -query dltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > dltA_on_${sample}.blastn
    158. done
    159. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    160.   blastn -db ../shovill/${sample}_contigs.fa -query fmtC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_${sample}.blastn
    161. done
    162. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    163.   blastn -db ../shovill/${sample}_contigs.fa -query lipA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > lipA_on_${sample}.blastn
    164. done
    165. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    166.   blastn -db ../shovill/${sample}_contigs.fa -query sceD.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_${sample}.blastn
    167. done
    168. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    169.   blastn -db ../shovill/${sample}_contigs.fa -query SE0760.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_${sample}.blastn
    170. done
    172. # -- Serine protease: esp, ecpA --
    173. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    174.   blastn -db ../shovill/${sample}_contigs.fa -query esp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./esp_on_${sample}.blastn
    175. done
    176. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    177.   blastn -db ../shovill/${sample}_contigs.fa -query ecpA_.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_${sample}.blastn
    178. done
    180. # -- Phage: PhiSepi-HH1, PI-Sepi-HH2, PhiSepi-HH3 (#HH1-HP1, HH3-HP2, HH3-TreR) --
    181. #34053 (3000,2510) 36164 (500) 147057 (6618, 15237+3812, 15237+3812, 15233+3814, 15230+3812)
    182. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    183.   blastn -db ../shovill/${sample}_contigs.fa -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./MT880870_on_${sample}.blastn
    184. done
    185. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    186.   blastn -db ../shovill/${sample}_contigs.fa -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./MT880871_on_${sample}.blastn
    187. done
    188. for sample in HDM1 HDM7 HDM10 HDM11-SF1 HDM15-SF2; do
    189.   blastn -db ../shovill/${sample}_contigs.fa -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_${sample}.blastn
    190. done

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