[2024-01-24 14:23:05,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:05,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:05,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference
[2024-01-24 14:23:06,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,687] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg66269408-4eb3-44c9-91a3-2cd58ecfa8f0/GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna.gz | prodigal -d GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/cds.fna -a GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:17,327] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:17,328] [INFO] Task started: HMMsearch
[2024-01-24 14:23:17,328] [INFO] Running command: hmmsearch --tblout GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference/reference_markers.hmm GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:17,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:17,565] [INFO] Found 6/6 markers.
[2024-01-24 14:23:17,589] [INFO] Query marker FASTA was written to GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/markers.fasta
[2024-01-24 14:23:17,590] [INFO] Task started: Blastn
[2024-01-24 14:23:17,590] [INFO] Running command: blastn -query GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/markers.fasta -db /var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference/reference_markers.fasta -out GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:18,273] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:18,277] [INFO] Selected 18 target genomes.
[2024-01-24 14:23:18,277] [INFO] Target genome list was writen to GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/target_genomes.txt
[2024-01-24 14:23:18,286] [INFO] Task started: fastANI
[2024-01-24 14:23:18,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg66269408-4eb3-44c9-91a3-2cd58ecfa8f0/GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna.gz --refList GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/target_genomes.txt --output GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:29,273] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:29,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:29,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:29,279] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:29,279] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:23:29,279] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Porphyromonas bobii	strain=EMRHCC_6C	GCA_943169685.1	2811780	2811780	type	True	100.0	751	752	95	inconclusive
Porphyromonas pasteri	strain=JCM 30531	GCA_014647755.1	1583331	1583331	type	True	96.1373	681	752	95	inconclusive
Porphyromonas catoniae	strain=ATCC 51270	GCA_000565015.1	41976	41976	type	True	78.6511	190	752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:29,281] [INFO] DFAST Taxonomy check result was written to GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/tc_result.tsv
[2024-01-24 14:23:29,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:29,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:29,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference/checkm_data
[2024-01-24 14:23:29,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:29,327] [INFO] Task started: CheckM
[2024-01-24 14:23:29,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/checkm_input GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/checkm_result
[2024-01-24 14:24:04,898] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:04,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:04,918] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:04,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:04,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/markers.fasta)
[2024-01-24 14:24:04,919] [INFO] Task started: Blastn
[2024-01-24 14:24:04,919] [INFO] Running command: blastn -query GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/markers.fasta -db /var/lib/cwl/stg04471c23-a8f9-4114-abe0-89c1a202deb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:05,793] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:05,797] [INFO] Selected 12 target genomes.
[2024-01-24 14:24:05,797] [INFO] Target genome list was writen to GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:05,808] [INFO] Task started: fastANI
[2024-01-24 14:24:05,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg66269408-4eb3-44c9-91a3-2cd58ecfa8f0/GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna.gz --refList GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/target_genomes_gtdb.txt --output GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:12,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:12,259] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:12,260] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014647755.1	s__Porphyromonas pasteri	96.1373	681	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.26	95.60	0.93	0.85	32	conclusive
GCF_000467855.2	s__Porphyromonas sp000467855	81.0061	449	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.77	96.77	0.93	0.93	2	-
GCF_018127745.1	s__Porphyromonas sp018127745	79.6151	305	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372525.1	s__Porphyromonas sp905372525	79.3505	292	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372565.1	s__Porphyromonas sp905372565	78.7344	260	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.78	96.78	0.93	0.93	2	-
GCF_000565015.1	s__Porphyromonas catoniae	78.6511	190	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.79	96.79	0.93	0.93	2	-
GCF_000769075.1	s__Porphyromonas sp000769075	77.3069	83	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.48	98.48	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:12,262] [INFO] GTDB search result was written to GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:12,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:12,266] [INFO] DFAST_QC result json was written to GCF_943169685.1_Porphyromonas_sp._bobii-EMRHCC_6C_genomic.fna/dqc_result.json
[2024-01-24 14:24:12,266] [INFO] DFAST_QC completed!
[2024-01-24 14:24:12,266] [INFO] Total running time: 0h1m7s