[2023-06-29 16:46:51,052] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:46:51,055] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:46:51,055] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference
[2023-06-29 16:46:52,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:46:52,353] [INFO] Task started: Prodigal
[2023-06-29 16:46:52,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg92870848-e782-43a9-8d14-53ec50f2e6fd/GCA_023401855.1_ASM2340185v1_genomic.fna.gz | prodigal -d GCA_023401855.1_ASM2340185v1_genomic.fna/cds.fna -a GCA_023401855.1_ASM2340185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:46:59,276] [INFO] Task succeeded: Prodigal
[2023-06-29 16:46:59,277] [INFO] Task started: HMMsearch
[2023-06-29 16:46:59,277] [INFO] Running command: hmmsearch --tblout GCA_023401855.1_ASM2340185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference/reference_markers.hmm GCA_023401855.1_ASM2340185v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:46:59,516] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:46:59,517] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg92870848-e782-43a9-8d14-53ec50f2e6fd/GCA_023401855.1_ASM2340185v1_genomic.fna.gz]
[2023-06-29 16:46:59,540] [INFO] Query marker FASTA was written to GCA_023401855.1_ASM2340185v1_genomic.fna/markers.fasta
[2023-06-29 16:46:59,540] [INFO] Task started: Blastn
[2023-06-29 16:46:59,540] [INFO] Running command: blastn -query GCA_023401855.1_ASM2340185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference/reference_markers.fasta -out GCA_023401855.1_ASM2340185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:00,145] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:00,150] [INFO] Selected 15 target genomes.
[2023-06-29 16:47:00,151] [INFO] Target genome list was writen to GCA_023401855.1_ASM2340185v1_genomic.fna/target_genomes.txt
[2023-06-29 16:47:00,155] [INFO] Task started: fastANI
[2023-06-29 16:47:00,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg92870848-e782-43a9-8d14-53ec50f2e6fd/GCA_023401855.1_ASM2340185v1_genomic.fna.gz --refList GCA_023401855.1_ASM2340185v1_genomic.fna/target_genomes.txt --output GCA_023401855.1_ASM2340185v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:47:09,796] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:09,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:47:09,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:47:09,811] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 16:47:09,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 16:47:09,811] [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
Sanguibacteroides justesenii	strain=OUH 308042	GCA_000832075.1	1547597	1547597	type	True	99.1781	350	356	95	conclusive
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	77.9732	69	356	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	77.864	72	356	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	77.7779	75	356	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	77.749	78	356	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	77.7372	79	356	95	below_threshold
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	77.6586	78	356	95	below_threshold
Butyricimonas faecalis	strain=H184	GCA_003991565.1	2093856	2093856	type	True	77.5791	83	356	95	below_threshold
Butyricimonas faecalis	strain=vagina	GCA_900258545.1	2093856	2093856	type	True	77.5307	84	356	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:47:09,815] [INFO] DFAST Taxonomy check result was written to GCA_023401855.1_ASM2340185v1_genomic.fna/tc_result.tsv
[2023-06-29 16:47:09,816] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:47:09,817] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:47:09,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference/checkm_data
[2023-06-29 16:47:09,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:47:09,843] [INFO] Task started: CheckM
[2023-06-29 16:47:09,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023401855.1_ASM2340185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023401855.1_ASM2340185v1_genomic.fna/checkm_input GCA_023401855.1_ASM2340185v1_genomic.fna/checkm_result
[2023-06-29 16:47:35,979] [INFO] Task succeeded: CheckM
[2023-06-29 16:47:35,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.69%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 16:47:36,001] [INFO] ===== Completeness check finished =====
[2023-06-29 16:47:36,001] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:47:36,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023401855.1_ASM2340185v1_genomic.fna/markers.fasta)
[2023-06-29 16:47:36,002] [INFO] Task started: Blastn
[2023-06-29 16:47:36,002] [INFO] Running command: blastn -query GCA_023401855.1_ASM2340185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6805516-4522-4e07-b830-303df442e03f/dqc_reference/reference_markers_gtdb.fasta -out GCA_023401855.1_ASM2340185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:36,840] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:36,845] [INFO] Selected 11 target genomes.
[2023-06-29 16:47:36,846] [INFO] Target genome list was writen to GCA_023401855.1_ASM2340185v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:47:36,881] [INFO] Task started: fastANI
[2023-06-29 16:47:36,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg92870848-e782-43a9-8d14-53ec50f2e6fd/GCA_023401855.1_ASM2340185v1_genomic.fna.gz --refList GCA_023401855.1_ASM2340185v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023401855.1_ASM2340185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:47:43,673] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:43,681] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:47:43,681] [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
GCA_001487125.1	s__Gabonibacter massiliensis	99.3461	347	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Gabonibacter	95.0	98.83	98.37	0.92	0.88	5	conclusive
GCA_900543425.1	s__Gabonibacter sp900543425	88.1615	335	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Gabonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479425.1	s__Butyricimonas sp003479425	78.2664	70	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
GCA_900761485.1	s__Butyricimonas sp900761485	77.9778	67	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519105.1	s__Butyricimonas virosa	77.864	72	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCF_011927845.1	s__Butyricimonas paravirosa	77.8591	77	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	-
GCF_014647335.1	s__Butyricimonas faecihominis	77.749	78	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCF_003991565.1	s__Butyricimonas faecalis	77.5791	83	356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	-
--------------------------------------------------------------------------------
[2023-06-29 16:47:43,683] [INFO] GTDB search result was written to GCA_023401855.1_ASM2340185v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:47:43,684] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:47:43,687] [INFO] DFAST_QC result json was written to GCA_023401855.1_ASM2340185v1_genomic.fna/dqc_result.json
[2023-06-29 16:47:43,687] [INFO] DFAST_QC completed!
[2023-06-29 16:47:43,687] [INFO] Total running time: 0h0m53s