[2024-01-24 11:05:26,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:26,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:26,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference
[2024-01-24 11:05:28,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:28,339] [INFO] Task started: Prodigal
[2024-01-24 11:05:28,339] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf9bc697-697d-4db8-81fa-a591341fff38/GCF_900637795.1_52592_H02_genomic.fna.gz | prodigal -d GCF_900637795.1_52592_H02_genomic.fna/cds.fna -a GCF_900637795.1_52592_H02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:38,176] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:38,176] [INFO] Task started: HMMsearch
[2024-01-24 11:05:38,176] [INFO] Running command: hmmsearch --tblout GCF_900637795.1_52592_H02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference/reference_markers.hmm GCF_900637795.1_52592_H02_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:38,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:38,460] [INFO] Found 6/6 markers.
[2024-01-24 11:05:38,482] [INFO] Query marker FASTA was written to GCF_900637795.1_52592_H02_genomic.fna/markers.fasta
[2024-01-24 11:05:38,482] [INFO] Task started: Blastn
[2024-01-24 11:05:38,482] [INFO] Running command: blastn -query GCF_900637795.1_52592_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference/reference_markers.fasta -out GCF_900637795.1_52592_H02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:39,156] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:39,159] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:39,160] [INFO] Target genome list was writen to GCF_900637795.1_52592_H02_genomic.fna/target_genomes.txt
[2024-01-24 11:05:39,189] [INFO] Task started: fastANI
[2024-01-24 11:05:39,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9bc697-697d-4db8-81fa-a591341fff38/GCF_900637795.1_52592_H02_genomic.fna.gz --refList GCF_900637795.1_52592_H02_genomic.fna/target_genomes.txt --output GCF_900637795.1_52592_H02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:48,240] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:48,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:48,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:48,249] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:48,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:48,249] [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
Weeksella virosa	strain=NCTC11634	GCA_900637795.1	1014	1014	type	True	100.0	760	762	95	conclusive
Weeksella virosa	strain=DSM 16922	GCA_000189415.1	1014	1014	type	True	99.9974	756	762	95	conclusive
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	77.7118	105	762	95	below_threshold
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	77.5575	107	762	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	77.2055	105	762	95	below_threshold
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	76.8825	117	762	95	below_threshold
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	76.8404	116	762	95	below_threshold
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	76.8302	120	762	95	below_threshold
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	76.7639	112	762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:48,251] [INFO] DFAST Taxonomy check result was written to GCF_900637795.1_52592_H02_genomic.fna/tc_result.tsv
[2024-01-24 11:05:48,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:48,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:48,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference/checkm_data
[2024-01-24 11:05:48,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:48,296] [INFO] Task started: CheckM
[2024-01-24 11:05:48,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637795.1_52592_H02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637795.1_52592_H02_genomic.fna/checkm_input GCF_900637795.1_52592_H02_genomic.fna/checkm_result
[2024-01-24 11:06:21,656] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:21,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:21,682] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:21,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:21,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637795.1_52592_H02_genomic.fna/markers.fasta)
[2024-01-24 11:06:21,683] [INFO] Task started: Blastn
[2024-01-24 11:06:21,683] [INFO] Running command: blastn -query GCF_900637795.1_52592_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3aa4a0e-427e-462c-ad09-3a374b906676/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637795.1_52592_H02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:22,762] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:22,766] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:22,767] [INFO] Target genome list was writen to GCF_900637795.1_52592_H02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:22,786] [INFO] Task started: fastANI
[2024-01-24 11:06:22,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9bc697-697d-4db8-81fa-a591341fff38/GCF_900637795.1_52592_H02_genomic.fna.gz --refList GCF_900637795.1_52592_H02_genomic.fna/target_genomes_gtdb.txt --output GCF_900637795.1_52592_H02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:32,567] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:32,583] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:32,584] [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_000189415.1	s__Weeksella virosa	99.9976	755	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Weeksella	95.0	99.69	99.41	0.96	0.94	4	conclusive
GCA_000751595.1	s__Weeksella massiliensis	87.162	630	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Weeksella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089075.1	s__Vaginella massiliensis	80.6907	229	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Vaginella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013488205.1	s__Empedobacter falsenii_A	77.7832	145	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.19	95.74	0.91	0.86	9	-
GCF_000382425.1	s__Empedobacter brevis	77.5575	107	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	98.11	96.51	0.89	0.85	7	-
GCA_002378465.1	s__Empedobacter sp002378465	77.4577	125	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.64	95.90	0.90	0.86	24	-
GCF_015234135.1	s__Faecalibacter rhinopitheci	77.208	104	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	98.99	98.99	0.97	0.97	2	-
GCF_900115015.1	s__Algoriella xinjiangensis	77.0674	128	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	-
GCF_013116755.1	s__Empedobacter stercoris	77.0045	134	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCA_003687725.1	s__Faecalibacter macacae	76.887	118	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785645.1	s__Empedobacter tilapiae	76.8273	120	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142565.1	s__Chishuiella changwenlii	76.7974	115	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:32,585] [INFO] GTDB search result was written to GCF_900637795.1_52592_H02_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:32,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:32,589] [INFO] DFAST_QC result json was written to GCF_900637795.1_52592_H02_genomic.fna/dqc_result.json
[2024-01-24 11:06:32,590] [INFO] DFAST_QC completed!
[2024-01-24 11:06:32,590] [INFO] Total running time: 0h1m6s