------------------- V I R O M A T C H ------------------- # adaptor: /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/adaptor/adaptor.fqtrim # bam: true # bitprox: 1 # bsize: 1 # config: /storage1/fs1/kwylie/Active/2020_09_21_AHA/redoPP2/test/CONFIG.yaml # dryrun: false # endqual: 10 # evalue: 0.001 # host: /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/host/GRCh38_latest_genomic.fna # input: # - /storage1/fs1/kwylie/Archive/2020_09_21_AHA_RAW_DATA_ONLY/RAW_DATA/gerald_HG3LNDSXY_4_GGTTGGAC-TACAGGAT.bam # keep: true # minn: 50 # mts: 5 # nr: # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-10.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-11.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-12.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-13.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-14.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-15.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-16.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-17.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-18.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-19.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-1.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-20.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-21.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-22.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-23.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-24.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-25.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-26.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-27.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-28.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-29.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-2.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-30.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-31.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-32.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-33.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-34.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-35.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-36.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-37.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-38.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-39.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-3.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-40.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-4.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-5.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-6.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-7.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-8.dmnd # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nr/nr-9.dmnd # nt: # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-10.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-11.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-12.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-13.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-14.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-15.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-16.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-17.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-18.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-19.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-1.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-20.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-21.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-22.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-23.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-24.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-25.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-26.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-27.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-28.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-29.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-2.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-30.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-31.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-32.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-33.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-34.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-35.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-36.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-37.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-38.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-39.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-3.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-40.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-41.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-42.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-43.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-44.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-45.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-46.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-47.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-48.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-49.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-4.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-50.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-51.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-52.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-53.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-54.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-55.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-56.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-57.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-58.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-59.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-5.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-60.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-61.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-62.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-63.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-64.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-65.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-66.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-67.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-68.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-69.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-6.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-70.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-71.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-72.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-73.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-74.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-7.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-8.fna # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/ncbi/nt/nt-9.fna # outdir: /storage1/fs1/kwylie/Active/2020_09_21_AHA/redoPP2/test/ # phred: 33 # pid: 0.15 # pidprox: 0.04 # readlen: 50 # sampleid: GAGATTCC-CCTATCCT_S58_L001 # smkcores: 1 # snakefile: /usr/lib/python3.7/viromatch/recipes/viromatch.smk # taxid: /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/taxonomy/taxonomy.tsv # variants: false # version: ViroMatch (Revision 45 / Build beta) # viralfaa: /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/viral-only/trans_nuc/ncbi_viral_refseq_gn_20191120.dmnd # viralfna: /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases/databases/viral-only/nuc/ncbi_viral_refseq_gn_20191120.fna # wustlconfig: /storage1/fs1/kwylie/Active/2020_09_21_AHA/redoPP2/run.yaml # docker: # image: twylie/vm:45 # volumes: # - /storage1/fs1/tnwylie_lab/Active/viroMatchDatabases:/storage1/fs1/tnwylie_lab/Active/viroMatchDatabases # - /storage1/fs1/kwylie/Active/2020_09_21_AHA/redoPP2:/storage1/fs1/kwylie/Active/2020_09_21_AHA/redoPP2 # - /storage1/fs1/kwylie/Archive/2020_09_21_AHA_RAW_DATA_ONLY/RAW_DATA:/storage1/fs1/kwylie/Archive/2020_09_21_AHA_RAW_DATA_ONLY/RAW_DATA # lsf: # compute group: compute-kwylie # cores: '150' # ignore hosts: # - compute1-exec-67.ris.wustl.edu # - compute1-exec-117.ris.wustl.edu # - compute1-exec-102.ris.wustl.edu # latency wait: '100' # local cores: '1' # log directory: /storage1/fs1/kwylie/Active/2020_09_21_AHA/redoPP2/test/lsf_logs/ # memory: 16G # queue: general # restart times: '3' :BEGIN: Sample ID: GAGATTCC-CCTATCCT_S58_L001 Date: October 30, 2020 =========================================================================== TRANSLATED NUCLEOTIDE ALIGNMENT READ COUNTS =========================================================================== LINEAGE (R1 + R2) -------------------- [1] read count [2] percent [3] lineage -------------------- 4 0.4 Viruses --> Caudovirales --> Podoviridae --> Autographivirinae --> unclassified Autographivirinae --> Pseudomonas phage PPpW-4 3 0.3 Viruses --> Caudovirales --> Siphoviridae --> unclassified Siphoviridae --> Streptococcus virus MS1 2 0.2 Viruses --> Caudovirales --> Podoviridae --> Picovirinae --> Cepunavirus --> Streptococcus virus Cp1 --> Streptococcus phage Cp-1 1 0.1 Viruses --> Riboviria --> Flaviviridae --> Pegivirus --> Pegivirus C --> GB virus C -------------------- 10 TOTAL GENUS (R1 + R2) -------------------- [1] read count [2] percent [3] genus -------------------- 4 0.4 unknown genus | Pseudomonas phage PPpW-4 3 0.3 unknown genus | Streptococcus virus MS1 2 0.2 Cepunavirus 1 0.1 Pegivirus -------------------- 10 TOTAL SPECIES (R1 + R2) -------------------- [1] read count [2] percent [3] species -------------------- 4 0.4 Pseudomonas phage PPpW-4 3 0.3 Streptococcus virus MS1 2 0.2 Streptococcus virus Cp1 1 0.1 Pegivirus C -------------------- 10 TOTAL ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: LINEAGE (R1) -------------------- [1] read count [2] percent [3] lineage -------------------- 3 0.6 Viruses --> Caudovirales --> Siphoviridae --> unclassified Siphoviridae --> Streptococcus virus MS1 2 0.4 Viruses --> Caudovirales --> Podoviridae --> Autographivirinae --> unclassified Autographivirinae --> Pseudomonas phage PPpW-4 -------------------- 5 TOTAL GENUS (R1) -------------------- [1] read count [2] percent [3] genus -------------------- 3 0.6 unknown genus | Streptococcus virus MS1 2 0.4 unknown genus | Pseudomonas phage PPpW-4 -------------------- 5 TOTAL SPECIES (R1) -------------------- [1] read count [2] percent [3] species -------------------- 3 0.6 Streptococcus virus MS1 2 0.4 Pseudomonas phage PPpW-4 -------------------- 5 TOTAL ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: LINEAGE (R2) -------------------- [1] read count [2] percent [3] lineage -------------------- 2 0.4 Viruses --> Caudovirales --> Podoviridae --> Autographivirinae --> unclassified Autographivirinae --> Pseudomonas phage PPpW-4 2 0.4 Viruses --> Caudovirales --> Podoviridae --> Picovirinae --> Cepunavirus --> Streptococcus virus Cp1 --> Streptococcus phage Cp-1 1 0.2 Viruses --> Riboviria --> Flaviviridae --> Pegivirus --> Pegivirus C --> GB virus C -------------------- 5 TOTAL GENUS (R2) -------------------- [1] read count [2] percent [3] genus -------------------- 2 0.4 Cepunavirus 2 0.4 unknown genus | Pseudomonas phage PPpW-4 1 0.2 Pegivirus -------------------- 5 TOTAL SPECIES (R2) -------------------- [1] read count [2] percent [3] species -------------------- 2 0.4 Streptococcus virus Cp1 2 0.4 Pseudomonas phage PPpW-4 1 0.2 Pegivirus C -------------------- 5 TOTAL :END: