[2024-01-24 15:32:06,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:06,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:06,010] [INFO] DQC Reference Directory: /var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference
[2024-01-24 15:32:07,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:07,206] [INFO] Task started: Prodigal
[2024-01-24 15:32:07,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9a0c204-96fb-4ef4-8eb3-184e143692c4/GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/cds.fna -a GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:29,851] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:29,852] [INFO] Task started: HMMsearch
[2024-01-24 15:32:29,852] [INFO] Running command: hmmsearch --tblout GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference/reference_markers.hmm GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:30,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:30,188] [INFO] Found 6/6 markers.
[2024-01-24 15:32:30,248] [INFO] Query marker FASTA was written to GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:32:30,249] [INFO] Task started: Blastn
[2024-01-24 15:32:30,249] [INFO] Running command: blastn -query GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference/reference_markers.fasta -out GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:31,548] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:31,552] [INFO] Selected 26 target genomes.
[2024-01-24 15:32:31,552] [INFO] Target genome list was writen to GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:32:31,593] [INFO] Task started: fastANI
[2024-01-24 15:32:31,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a0c204-96fb-4ef4-8eb3-184e143692c4/GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna.gz --refList GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:33:19,808] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:19,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:33:19,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:33:19,827] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:33:19,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:33:19,828] [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
Streptomyces jietaisiensis	strain=CGMCC 4.1859	GCA_900102095.1	235987	235987	type	True	100.0	2534	2537	95	conclusive
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.1027	1445	2537	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	84.0861	1534	2537	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	84.0089	1529	2537	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	83.9865	1525	2537	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	83.9278	1484	2537	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	83.8765	1513	2537	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	83.7514	1541	2537	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.6886	1515	2537	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	83.6487	1489	2537	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	83.6481	1483	2537	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	83.6288	1497	2537	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	83.6207	1518	2537	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	83.5827	1609	2537	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	83.5387	1273	2537	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	83.4129	1545	2537	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	83.4005	1497	2537	95	below_threshold
Streptomyces prasinopilosus	strain=NRRL B-2711	GCA_001419695.1	67344	67344	type	True	83.364	1008	2537	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	83.3606	1480	2537	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	83.3204	1291	2537	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	83.3006	1373	2537	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	83.2688	1262	2537	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	83.2397	1395	2537	95	below_threshold
Streptomyces prasinus	strain=NRRL B-2712	GCA_001419705.1	67345	67345	type	True	83.158	1191	2537	95	below_threshold
Streptomyces malaysiense	strain=MUSC 136	GCA_000980885.2	1428626	1428626	type	True	83.0372	1399	2537	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.9874	1540	2537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:33:19,830] [INFO] DFAST Taxonomy check result was written to GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:33:19,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:33:19,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:33:19,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference/checkm_data
[2024-01-24 15:33:19,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:33:19,914] [INFO] Task started: CheckM
[2024-01-24 15:33:19,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/checkm_input GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:35:16,318] [INFO] Task succeeded: CheckM
[2024-01-24 15:35:16,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:35:16,350] [INFO] ===== Completeness check finished =====
[2024-01-24 15:35:16,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:35:16,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:35:16,351] [INFO] Task started: Blastn
[2024-01-24 15:35:16,351] [INFO] Running command: blastn -query GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgadae3d47-2731-4676-8762-e73d145f7051/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:35:18,524] [INFO] Task succeeded: Blastn
[2024-01-24 15:35:18,528] [INFO] Selected 22 target genomes.
[2024-01-24 15:35:18,529] [INFO] Target genome list was writen to GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:35:18,586] [INFO] Task started: fastANI
[2024-01-24 15:35:18,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a0c204-96fb-4ef4-8eb3-184e143692c4/GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna.gz --refList GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:36:04,233] [INFO] Task succeeded: fastANI
[2024-01-24 15:36:04,251] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:36:04,251] [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
GCA_014656015.1	s__Streptomyces griseoaurantiacus	98.988	2288	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.09	98.94	0.94	0.90	5	conclusive
GCF_000725625.1	s__Streptomyces sp000725625	90.5126	2031	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	4	-
GCF_014650575.1	s__Streptomyces naganishii	84.0722	1536	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	84.0293	1525	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	83.9667	1529	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	83.9016	1554	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_013364255.1	s__Streptomyces seoulensis_A	83.8988	1550	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	83.8868	1511	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	83.75	1542	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_003369795.1	s__Streptomyces sp003369795	83.7137	1526	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	83.6982	1519	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237655.1	s__Streptomyces sp002237655	83.6551	1521	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074055.1	s__Streptomyces nigra	83.6324	1493	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	-
GCF_014651155.1	s__Streptomyces anthocyanicus	83.588	1605	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCF_001267885.1	s__Streptomyces ambofaciens	83.5863	1525	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_017526105.1	s__Streptomyces cyanogenus	83.4859	1489	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	83.4471	1497	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_014649115.1	s__Streptomyces eurythermus	83.4183	1493	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_001418415.1	s__Streptomyces hirsutus	83.2839	1261	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.60	97.60	0.78	0.78	2	-
GCF_004784465.1	s__Streptomyces griseoluteus	83.2203	1398	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_001419705.1	s__Streptomyces prasinus	83.1973	1185	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.87	97.75	0.84	0.80	4	-
GCF_003143935.1	s__Streptomyces sp003143935	83.1366	1549	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:36:04,253] [INFO] GTDB search result was written to GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:36:04,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:36:04,260] [INFO] DFAST_QC result json was written to GCF_900102095.1_IMG-taxon_2667527442_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:36:04,260] [INFO] DFAST_QC completed!
[2024-01-24 15:36:04,260] [INFO] Total running time: 0h3m58s