[2024-01-24 12:46:49,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:49,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:49,774] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference
[2024-01-24 12:46:50,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:50,936] [INFO] Task started: Prodigal
[2024-01-24 12:46:50,936] [INFO] Running command: gunzip -c /var/lib/cwl/stgab45b60a-8cdd-4fe5-867c-2e8c27f2994b/GCF_002954765.1_ASM295476v1_genomic.fna.gz | prodigal -d GCF_002954765.1_ASM295476v1_genomic.fna/cds.fna -a GCF_002954765.1_ASM295476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:01,103] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:01,103] [INFO] Task started: HMMsearch
[2024-01-24 12:47:01,104] [INFO] Running command: hmmsearch --tblout GCF_002954765.1_ASM295476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference/reference_markers.hmm GCF_002954765.1_ASM295476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:01,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:01,349] [INFO] Found 6/6 markers.
[2024-01-24 12:47:01,380] [INFO] Query marker FASTA was written to GCF_002954765.1_ASM295476v1_genomic.fna/markers.fasta
[2024-01-24 12:47:01,381] [INFO] Task started: Blastn
[2024-01-24 12:47:01,381] [INFO] Running command: blastn -query GCF_002954765.1_ASM295476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference/reference_markers.fasta -out GCF_002954765.1_ASM295476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:02,008] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:02,012] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:02,012] [INFO] Target genome list was writen to GCF_002954765.1_ASM295476v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:02,019] [INFO] Task started: fastANI
[2024-01-24 12:47:02,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgab45b60a-8cdd-4fe5-867c-2e8c27f2994b/GCF_002954765.1_ASM295476v1_genomic.fna.gz --refList GCF_002954765.1_ASM295476v1_genomic.fna/target_genomes.txt --output GCF_002954765.1_ASM295476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:10,810] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:10,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:10,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:10,822] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:10,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:10,822] [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
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	100.0	1104	1107	95	conclusive
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	89.1041	921	1107	95	below_threshold
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	89.0205	927	1107	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	79.5157	401	1107	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	79.271	387	1107	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	78.5532	353	1107	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	78.5082	360	1107	95	below_threshold
Nonlabens tegetincola	strain=JCM 12886	GCA_002954355.1	323273	323273	type	True	77.9179	218	1107	95	below_threshold
Nonlabens agnitus	strain=JCM 17109	GCA_002994045.1	870484	870484	type	True	77.3087	182	1107	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.8745	79	1107	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.4703	75	1107	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.4385	72	1107	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.0742	70	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:10,824] [INFO] DFAST Taxonomy check result was written to GCF_002954765.1_ASM295476v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:10,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:10,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:10,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference/checkm_data
[2024-01-24 12:47:10,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:10,859] [INFO] Task started: CheckM
[2024-01-24 12:47:10,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954765.1_ASM295476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954765.1_ASM295476v1_genomic.fna/checkm_input GCF_002954765.1_ASM295476v1_genomic.fna/checkm_result
[2024-01-24 12:47:44,041] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:44,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:44,059] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:44,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:44,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954765.1_ASM295476v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:44,060] [INFO] Task started: Blastn
[2024-01-24 12:47:44,060] [INFO] Running command: blastn -query GCF_002954765.1_ASM295476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe2e3ed1-e9e2-4758-b23f-0b93e5239e75/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954765.1_ASM295476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:44,867] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:44,870] [INFO] Selected 8 target genomes.
[2024-01-24 12:47:44,870] [INFO] Target genome list was writen to GCF_002954765.1_ASM295476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:44,878] [INFO] Task started: fastANI
[2024-01-24 12:47:44,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgab45b60a-8cdd-4fe5-867c-2e8c27f2994b/GCF_002954765.1_ASM295476v1_genomic.fna.gz --refList GCF_002954765.1_ASM295476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954765.1_ASM295476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:50,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:50,522] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:50,522] [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_002954765.1	s__Nonlabens arenilitoris	100.0	1104	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000732625.1	s__Nonlabens ulvanivorans	89.1062	921	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	98.59	98.07	0.92	0.89	5	-
GCF_000755285.1	s__Nonlabens ulvanivorans_A	88.6236	885	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.55	97.55	0.94	0.94	2	-
GCA_000153385.1	s__Nonlabens sp000153385	86.5771	868	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934445.1	s__Nonlabens xylanidelens	79.2857	386	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002162835.1	s__Nonlabens dokdonensis_B	78.6676	309	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	78.4951	361	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012974865.1	s__Nonlabens sp012974865	78.0849	287	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:50,524] [INFO] GTDB search result was written to GCF_002954765.1_ASM295476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:50,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:50,529] [INFO] DFAST_QC result json was written to GCF_002954765.1_ASM295476v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:50,529] [INFO] DFAST_QC completed!
[2024-01-24 12:47:50,529] [INFO] Total running time: 0h1m1s