[2024-01-25 18:11:20,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:20,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:20,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference
[2024-01-25 18:11:21,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:21,754] [INFO] Task started: Prodigal
[2024-01-25 18:11:21,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg26ed7802-5a2d-4746-8da9-9760e465cf2a/GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/cds.fna -a GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:40,876] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:40,877] [INFO] Task started: HMMsearch
[2024-01-25 18:11:40,877] [INFO] Running command: hmmsearch --tblout GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference/reference_markers.hmm GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:41,186] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:41,187] [INFO] Found 6/6 markers.
[2024-01-25 18:11:41,241] [INFO] Query marker FASTA was written to GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:11:41,241] [INFO] Task started: Blastn
[2024-01-25 18:11:41,242] [INFO] Running command: blastn -query GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference/reference_markers.fasta -out GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:42,449] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:42,452] [INFO] Selected 19 target genomes.
[2024-01-25 18:11:42,453] [INFO] Target genome list was writen to GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:11:42,483] [INFO] Task started: fastANI
[2024-01-25 18:11:42,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ed7802-5a2d-4746-8da9-9760e465cf2a/GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna.gz --refList GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:20,037] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:20,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:20,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:20,051] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:20,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:20,052] [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 auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	100.0	2251	2252	95	conclusive
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	88.7759	1652	2252	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	88.6095	1633	2252	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	88.406	1613	2252	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	88.2297	1617	2252	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	88.1834	1597	2252	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	87.9817	1508	2252	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	87.6615	1422	2252	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	87.6369	1203	2252	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	87.5402	1642	2252	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	87.4447	1610	2252	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	87.3953	1488	2252	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	87.08	1547	2252	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	87.0115	1496	2252	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	86.664	1540	2252	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.8774	1115	2252	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.4889	1483	2252	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.1998	1269	2252	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.3705	620	2252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:20,054] [INFO] DFAST Taxonomy check result was written to GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:12:20,055] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:20,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:20,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference/checkm_data
[2024-01-25 18:12:20,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:20,122] [INFO] Task started: CheckM
[2024-01-25 18:12:20,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/checkm_input GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:14:12,160] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:12,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:12,178] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:12,179] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:12,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:14:12,180] [INFO] Task started: Blastn
[2024-01-25 18:14:12,180] [INFO] Running command: blastn -query GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg621bccda-2f36-44c6-9420-4ec38ce91f2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:14,082] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:14,084] [INFO] Selected 17 target genomes.
[2024-01-25 18:14:14,084] [INFO] Target genome list was writen to GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:14,108] [INFO] Task started: fastANI
[2024-01-25 18:14:14,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ed7802-5a2d-4746-8da9-9760e465cf2a/GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna.gz --refList GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:49,514] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:49,526] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:49,527] [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_900089595.1	s__Micromonospora auratinigra	100.0	2251	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003725545.1	s__Micromonospora sp003725545	89.5338	1436	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_014648395.1	s__Micromonospora fulviviridis	88.723	1659	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091475.1	s__Micromonospora chersina	88.5888	1636	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_008868175.1	s__Micromonospora sp008868175	88.4083	1453	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	88.3934	1614	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_000982955.1	s__Micromonospora sp000982955	88.2867	1509	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089605.1	s__Micromonospora narathiwatensis	87.9665	1508	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091545.1	s__Micromonospora viridifaciens	87.7222	1413	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008119785.1	s__Micromonospora sp008119785	87.7169	1549	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	87.6865	1198	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090105.1	s__Micromonospora humi	87.4038	1616	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090225.1	s__Micromonospora eburnea	87.3866	1489	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002926165.1	s__Micromonospora chalcea	87.0913	1486	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900091565.1	s__Micromonospora marina	86.6652	1426	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	-
GCF_900090245.1	s__Micromonospora halophytica	86.3889	1445	2252	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	85.5085	1431	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:49,529] [INFO] GTDB search result was written to GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:49,529] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:49,533] [INFO] DFAST_QC result json was written to GCF_900089595.1_IMG-taxon_2617270871_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:14:49,533] [INFO] DFAST_QC completed!
[2024-01-25 18:14:49,533] [INFO] Total running time: 0h3m29s