[2024-01-24 13:57:13,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,148] [INFO] DQC Reference Directory: /var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference
[2024-01-24 13:57:14,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,428] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,428] [INFO] Running command: gunzip -c /var/lib/cwl/stga87846bd-388d-4ec5-98c7-3573b342a9ba/GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/cds.fna -a GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:25,085] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:25,085] [INFO] Task started: HMMsearch
[2024-01-24 13:57:25,086] [INFO] Running command: hmmsearch --tblout GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference/reference_markers.hmm GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:25,352] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:25,354] [INFO] Found 6/6 markers.
[2024-01-24 13:57:25,395] [INFO] Query marker FASTA was written to GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:25,396] [INFO] Task started: Blastn
[2024-01-24 13:57:25,396] [INFO] Running command: blastn -query GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference/reference_markers.fasta -out GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:26,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:26,101] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:26,102] [INFO] Target genome list was writen to GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:26,106] [INFO] Task started: fastANI
[2024-01-24 13:57:26,106] [INFO] Running command: fastANI --query /var/lib/cwl/stga87846bd-388d-4ec5-98c7-3573b342a9ba/GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna.gz --refList GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:34,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:34,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:34,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:34,720] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:34,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:34,721] [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
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	100.0	1200	1205	95	conclusive
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	92.0799	988	1205	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	92.0045	994	1205	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	91.9822	995	1205	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	80.3007	603	1205	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	79.7325	570	1205	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.4049	383	1205	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.7545	387	1205	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.6794	314	1205	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.577	214	1205	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3689	189	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:34,722] [INFO] DFAST Taxonomy check result was written to GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:34,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:34,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:34,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference/checkm_data
[2024-01-24 13:57:34,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:34,760] [INFO] Task started: CheckM
[2024-01-24 13:57:34,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/checkm_input GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:58:11,574] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:11,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,596] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:11,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:11,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:58:11,597] [INFO] Task started: Blastn
[2024-01-24 13:58:11,597] [INFO] Running command: blastn -query GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d64f43-3b14-435e-b2c2-63228f874019/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:12,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:12,678] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:12,679] [INFO] Target genome list was writen to GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:12,704] [INFO] Task started: fastANI
[2024-01-24 13:58:12,704] [INFO] Running command: fastANI --query /var/lib/cwl/stga87846bd-388d-4ec5-98c7-3573b342a9ba/GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna.gz --refList GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:23,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:23,269] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:23,270] [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_900112595.1	s__Algibacter_B pectinivorans	100.0	1200	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014202225.1	s__Algibacter_B amylolyticus	92.0799	988	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003143755.1	s__Algibacter_B sp003143755	80.2869	604	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	80.0069	455	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	79.7407	568	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114265.1	s__Flaviramulus basaltis	79.5598	532	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	79.2339	541	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	79.1652	485	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.058	492	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	79.01	475	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	78.4113	383	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	78.4097	325	1205	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,271] [INFO] GTDB search result was written to GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:23,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:23,276] [INFO] DFAST_QC result json was written to GCF_900112595.1_IMG-taxon_2615840709_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:58:23,276] [INFO] DFAST_QC completed!
[2024-01-24 13:58:23,276] [INFO] Total running time: 0h1m10s