[2024-01-24 15:26:47,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:47,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:47,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference
[2024-01-24 15:26:49,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:49,102] [INFO] Task started: Prodigal
[2024-01-24 15:26:49,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b36bb56-05f1-4221-8dd6-4a28471e7001/GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/cds.fna -a GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:57,626] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:57,626] [INFO] Task started: HMMsearch
[2024-01-24 15:26:57,627] [INFO] Running command: hmmsearch --tblout GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference/reference_markers.hmm GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:57,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:57,902] [INFO] Found 6/6 markers.
[2024-01-24 15:26:57,932] [INFO] Query marker FASTA was written to GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:26:57,932] [INFO] Task started: Blastn
[2024-01-24 15:26:57,933] [INFO] Running command: blastn -query GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference/reference_markers.fasta -out GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:58,603] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:58,607] [INFO] Selected 16 target genomes.
[2024-01-24 15:26:58,607] [INFO] Target genome list was writen to GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:26:58,619] [INFO] Task started: fastANI
[2024-01-24 15:26:58,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b36bb56-05f1-4221-8dd6-4a28471e7001/GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna.gz --refList GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:08,441] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:08,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:08,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:08,462] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:08,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:08,462] [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
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	100.0	1068	1070	95	conclusive
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	81.0648	589	1070	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	80.9867	591	1070	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	78.9912	512	1070	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	78.5705	357	1070	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	77.1757	256	1070	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.9443	194	1070	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.9182	195	1070	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.8199	146	1070	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.7573	159	1070	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6727	109	1070	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	76.6539	138	1070	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.6009	119	1070	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.5846	155	1070	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	76.3248	111	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,464] [INFO] DFAST Taxonomy check result was written to GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:27:08,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:08,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:08,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference/checkm_data
[2024-01-24 15:27:08,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,502] [INFO] Task started: CheckM
[2024-01-24 15:27:08,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/checkm_input GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:27:38,586] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:38,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,607] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:38,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:38,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:27:38,609] [INFO] Task started: Blastn
[2024-01-24 15:27:38,609] [INFO] Running command: blastn -query GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4206f7d6-3498-4a4f-a37a-4bc196014d2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:39,607] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:39,611] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:39,611] [INFO] Target genome list was writen to GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:39,627] [INFO] Task started: fastANI
[2024-01-24 15:27:39,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b36bb56-05f1-4221-8dd6-4a28471e7001/GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna.gz --refList GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:48,390] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:48,402] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:48,402] [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_900141885.1	s__Mesonia phycicola	100.0	1068	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423405.1	s__Mesonia mobilis	80.9954	590	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_012964435.1	s__Mesonia sp012964435	80.266	541	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_008692195.1	s__Mesonia sp008692195	79.7058	512	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499555.1	s__Mesonia oceanica	78.9781	514	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_003253545.1	s__Mesonia algae	78.5588	358	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCF_003667275.1	s__Mesonia aquimarina	77.8094	333	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.1431	205	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233725.1	s__Mesonia sp003233725	76.8942	181	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	76.6612	219	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_002163675.1	s__Polaribacter sp002163675	76.6139	166	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632745.1	s__Aquimarina aggregata	76.5869	155	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_002201235.1	s__Polaribacter tangerinus	76.2815	114	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:48,404] [INFO] GTDB search result was written to GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:48,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:48,408] [INFO] DFAST_QC result json was written to GCF_900141885.1_IMG-taxon_2622736520_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:27:48,409] [INFO] DFAST_QC completed!
[2024-01-24 15:27:48,409] [INFO] Total running time: 0h1m1s