[2024-01-25 19:44:50,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:50,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:50,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference
[2024-01-25 19:44:51,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:51,650] [INFO] Task started: Prodigal
[2024-01-25 19:44:51,650] [INFO] Running command: gunzip -c /var/lib/cwl/stgf87e200d-1d8b-4498-8714-e13172427068/GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/cds.fna -a GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:06,849] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:06,849] [INFO] Task started: HMMsearch
[2024-01-25 19:45:06,849] [INFO] Running command: hmmsearch --tblout GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference/reference_markers.hmm GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:07,159] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:07,162] [INFO] Found 6/6 markers.
[2024-01-25 19:45:07,208] [INFO] Query marker FASTA was written to GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:45:07,209] [INFO] Task started: Blastn
[2024-01-25 19:45:07,209] [INFO] Running command: blastn -query GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference/reference_markers.fasta -out GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:08,351] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:08,354] [INFO] Selected 16 target genomes.
[2024-01-25 19:45:08,354] [INFO] Target genome list was writen to GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:45:08,364] [INFO] Task started: fastANI
[2024-01-25 19:45:08,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87e200d-1d8b-4498-8714-e13172427068/GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna.gz --refList GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:36,977] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:36,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:36,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:36,987] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:36,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:36,988] [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
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	100.0	1977	1982	95	conclusive
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	94.424	1688	1982	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	94.289	1679	1982	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	94.0114	1576	1982	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	92.8439	1567	1982	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	89.4033	1547	1982	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	89.2854	1139	1982	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	89.0205	1531	1982	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.6449	1315	1982	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.2577	1166	1982	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	83.94	1278	1982	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3769	1226	1982	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.3181	1239	1982	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.2853	1242	1982	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.2758	1227	1982	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.4253	569	1982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:36,989] [INFO] DFAST Taxonomy check result was written to GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:45:36,989] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:36,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:36,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference/checkm_data
[2024-01-25 19:45:36,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:37,045] [INFO] Task started: CheckM
[2024-01-25 19:45:37,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/checkm_input GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:46:44,585] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:44,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:44,603] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:44,603] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:44,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:46:44,605] [INFO] Task started: Blastn
[2024-01-25 19:46:44,605] [INFO] Running command: blastn -query GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa054e6c-b80f-4d93-9cfe-5a06cb00cf35/dqc_reference/reference_markers_gtdb.fasta -out GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:46,412] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:46,414] [INFO] Selected 15 target genomes.
[2024-01-25 19:46:46,414] [INFO] Target genome list was writen to GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:46,436] [INFO] Task started: fastANI
[2024-01-25 19:46:46,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87e200d-1d8b-4498-8714-e13172427068/GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna.gz --refList GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:15,201] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:15,211] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:15,211] [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_900091565.1	s__Micromonospora marina	100.0	1977	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	conclusive
GCF_000145235.1	s__Micromonospora aurantiaca	94.434	1688	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_900091605.1	s__Micromonospora tulbaghiae	94.0197	1575	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_002926165.1	s__Micromonospora chalcea	92.8439	1567	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900089585.1	s__Micromonospora sediminicola	89.425	1544	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_902825405.1	s__Micromonospora maritima	89.2712	1140	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003027925.1	s__Micromonospora sp003027925	88.7522	1510	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140155.1	s__Micromonospora sp002140155	88.6823	1462	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089595.1	s__Micromonospora auratinigra	86.8501	1414	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	86.8126	1259	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_018070575.1	s__Micromonospora sp018070575	84.8178	1361	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908295.1	s__Micromonospora rubida	84.7552	1333	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034245.1	s__Micromonospora sp012034245	84.4943	1276	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857055.1	s__Micromonospora inaquosa	83.7779	1170	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010560025.1	s__Micromonospora sp010560025	83.5122	1216	1982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:15,212] [INFO] GTDB search result was written to GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:15,213] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:15,216] [INFO] DFAST_QC result json was written to GCF_900091565.1_IMG-taxon_2622736534_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:47:15,216] [INFO] DFAST_QC completed!
[2024-01-25 19:47:15,216] [INFO] Total running time: 0h2m25s