[2024-01-24 13:12:52,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference
[2024-01-24 13:12:53,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,576] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg905a3229-2cfb-45ba-b0a9-357f96e8cc26/GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/cds.fna -a GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:14,679] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:14,679] [INFO] Task started: HMMsearch
[2024-01-24 13:13:14,679] [INFO] Running command: hmmsearch --tblout GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference/reference_markers.hmm GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:15,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:15,047] [INFO] Found 6/6 markers.
[2024-01-24 13:13:15,107] [INFO] Query marker FASTA was written to GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:15,107] [INFO] Task started: Blastn
[2024-01-24 13:13:15,107] [INFO] Running command: blastn -query GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference/reference_markers.fasta -out GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:16,387] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:16,391] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:16,391] [INFO] Target genome list was writen to GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:16,401] [INFO] Task started: fastANI
[2024-01-24 13:13:16,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg905a3229-2cfb-45ba-b0a9-357f96e8cc26/GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna.gz --refList GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:58,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:58,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:58,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:58,056] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:58,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:58,056] [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 coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	100.0	2255	2256	95	conclusive
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	93.8842	1717	2256	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	89.2238	1629	2256	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	88.8571	1642	2256	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	86.9542	1482	2256	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.666	1145	2256	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	86.6635	1435	2256	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	86.5706	1494	2256	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	86.5159	1555	2256	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	86.448	1466	2256	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	86.2766	1510	2256	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	86.1564	1515	2256	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	86.1358	1507	2256	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	86.0899	1516	2256	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	86.0508	1530	2256	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	86.0165	1523	2256	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	85.9995	1446	2256	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.6043	1295	2256	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.0934	1328	2256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:58,058] [INFO] DFAST Taxonomy check result was written to GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:13:58,058] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:58,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:58,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference/checkm_data
[2024-01-24 13:13:58,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:58,125] [INFO] Task started: CheckM
[2024-01-24 13:13:58,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/checkm_input GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:15:28,819] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:28,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:28,844] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:28,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:28,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:15:28,846] [INFO] Task started: Blastn
[2024-01-24 13:15:28,846] [INFO] Running command: blastn -query GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf30355cb-d864-4b20-b4de-8a557148449e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:30,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:30,793] [INFO] Selected 16 target genomes.
[2024-01-24 13:15:30,793] [INFO] Target genome list was writen to GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:30,803] [INFO] Task started: fastANI
[2024-01-24 13:15:30,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg905a3229-2cfb-45ba-b0a9-357f96e8cc26/GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna.gz --refList GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:04,134] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:04,150] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:04,150] [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_900090295.1	s__Micromonospora coxensis	100.0	2254	2256	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_900090245.1	s__Micromonospora halophytica	93.9065	1715	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	88.8851	1640	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_004348595.1	s__Micromonospora sp004348595	88.7078	1318	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348675.1	s__Micromonospora sp004348675	88.367	1248	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348325.1	s__Micromonospora sp004348325	87.9898	1271	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.89	97.89	0.85	0.85	2	-
GCF_004217615.1	s__Micromonospora kangleipakensis	86.9927	1477	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	86.6382	1340	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_016598485.1	s__Micromonospora veneta	86.6124	1442	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	86.4809	1559	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900090265.1	s__Micromonospora rifamycinica	86.4412	1468	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008868175.1	s__Micromonospora sp008868175	86.3584	1398	2256	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	86.2537	1512	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900091595.1	s__Micromonospora haikouensis	86.1215	1519	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_014205165.1	s__Micromonospora carbonacea	86.0878	1526	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900089605.1	s__Micromonospora narathiwatensis	85.9872	1446	2256	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:16:04,152] [INFO] GTDB search result was written to GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:04,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:04,157] [INFO] DFAST_QC result json was written to GCF_900090295.1_IMG-taxon_2623620609_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:16:04,157] [INFO] DFAST_QC completed!
[2024-01-24 13:16:04,157] [INFO] Total running time: 0h3m12s