[2024-01-24 12:37:09,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference
[2024-01-24 12:37:11,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,037] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,037] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc9f735f-6dc5-4b61-a5c8-7925595a7284/GCF_016863635.1_ASM1686363v1_genomic.fna.gz | prodigal -d GCF_016863635.1_ASM1686363v1_genomic.fna/cds.fna -a GCF_016863635.1_ASM1686363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:54,459] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:54,459] [INFO] Task started: HMMsearch
[2024-01-24 12:37:54,460] [INFO] Running command: hmmsearch --tblout GCF_016863635.1_ASM1686363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference/reference_markers.hmm GCF_016863635.1_ASM1686363v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:54,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:54,988] [INFO] Found 6/6 markers.
[2024-01-24 12:37:55,099] [INFO] Query marker FASTA was written to GCF_016863635.1_ASM1686363v1_genomic.fna/markers.fasta
[2024-01-24 12:37:55,100] [INFO] Task started: Blastn
[2024-01-24 12:37:55,100] [INFO] Running command: blastn -query GCF_016863635.1_ASM1686363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference/reference_markers.fasta -out GCF_016863635.1_ASM1686363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:56,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:56,351] [INFO] Selected 22 target genomes.
[2024-01-24 12:37:56,352] [INFO] Target genome list was writen to GCF_016863635.1_ASM1686363v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:56,362] [INFO] Task started: fastANI
[2024-01-24 12:37:56,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc9f735f-6dc5-4b61-a5c8-7925595a7284/GCF_016863635.1_ASM1686363v1_genomic.fna.gz --refList GCF_016863635.1_ASM1686363v1_genomic.fna/target_genomes.txt --output GCF_016863635.1_ASM1686363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:38,661] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:38,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:38,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:38,681] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:38,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:38,681] [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
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	100.0	4582	4594	95	conclusive
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	85.3973	2549	4594	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	78.6139	1656	4594	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	78.0192	897	4594	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	77.799	983	4594	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	77.7333	1018	4594	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	77.7079	1151	4594	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.6503	1199	4594	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	77.6042	1023	4594	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	77.5996	1008	4594	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	77.5551	1050	4594	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	77.5544	1036	4594	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	77.5061	1253	4594	95	below_threshold
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	77.4727	1067	4594	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	77.4708	1060	4594	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	77.4696	1111	4594	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	77.4353	1202	4594	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	77.4348	1080	4594	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	77.2899	1297	4594	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	77.2519	1307	4594	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	76.9085	1236	4594	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.169	873	4594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:38,683] [INFO] DFAST Taxonomy check result was written to GCF_016863635.1_ASM1686363v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:38,684] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:38,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:38,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference/checkm_data
[2024-01-24 12:38:38,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:38,811] [INFO] Task started: CheckM
[2024-01-24 12:38:38,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863635.1_ASM1686363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863635.1_ASM1686363v1_genomic.fna/checkm_input GCF_016863635.1_ASM1686363v1_genomic.fna/checkm_result
[2024-01-24 12:41:21,472] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:21,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.26%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2024-01-24 12:41:21,508] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:21,508] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:21,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863635.1_ASM1686363v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:21,509] [INFO] Task started: Blastn
[2024-01-24 12:41:21,509] [INFO] Running command: blastn -query GCF_016863635.1_ASM1686363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35417300-7303-4bb5-b8d7-da42e5e6d206/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863635.1_ASM1686363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:23,358] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:23,362] [INFO] Selected 20 target genomes.
[2024-01-24 12:41:23,363] [INFO] Target genome list was writen to GCF_016863635.1_ASM1686363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:23,377] [INFO] Task started: fastANI
[2024-01-24 12:41:23,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc9f735f-6dc5-4b61-a5c8-7925595a7284/GCF_016863635.1_ASM1686363v1_genomic.fna.gz --refList GCF_016863635.1_ASM1686363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863635.1_ASM1686363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:02,540] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:02,562] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:02,562] [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_016863635.1	s__Virgisporangium aurantiacum	100.0	4582	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016863655.1	s__Virgisporangium ochraceum	85.3511	2562	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863615.1	s__Virgisporangium aliadipatigenens	78.6281	1650	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	78.014	898	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	77.9936	1033	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	77.8055	981	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172955.1	s__Micromonospora sp003172955	77.7677	1007	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868155.1	s__Micromonospora sp008868155	77.7487	1007	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000145235.1	s__Micromonospora aurantiaca	77.6529	1207	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_900109115.1	s__Micromonospora phaseoli	77.5832	1024	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_012034245.1	s__Micromonospora sp012034245	77.5745	1024	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	77.5711	1045	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	77.4675	1110	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	77.3477	1071	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885555.1	s__Rugosimonospora sp005885555	77.3295	1047	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720365.1	s__Catellatospora paridis	77.2944	1294	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091625.1	s__Micromonospora peucetia	77.2701	1119	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	77.253	1346	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016880465.1	s__EFPC-2 sp016880465	77.2235	638	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__EFPC-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717135.1	s__Catenuloplanes japonicus	76.8741	1413	4594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:02,564] [INFO] GTDB search result was written to GCF_016863635.1_ASM1686363v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:02,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:02,569] [INFO] DFAST_QC result json was written to GCF_016863635.1_ASM1686363v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:02,569] [INFO] DFAST_QC completed!
[2024-01-24 12:42:02,569] [INFO] Total running time: 0h4m53s