[2024-01-24 14:39:01,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,527] [INFO] DQC Reference Directory: /var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference
[2024-01-24 14:39:04,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,258] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,259] [INFO] Running command: gunzip -c /var/lib/cwl/stg43e30f61-bdfc-40b4-8bcd-1cf0e7805bae/GCF_009604385.1_ASM960438v1_genomic.fna.gz | prodigal -d GCF_009604385.1_ASM960438v1_genomic.fna/cds.fna -a GCF_009604385.1_ASM960438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:26,559] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:26,559] [INFO] Task started: HMMsearch
[2024-01-24 14:39:26,559] [INFO] Running command: hmmsearch --tblout GCF_009604385.1_ASM960438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference/reference_markers.hmm GCF_009604385.1_ASM960438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:26,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:26,947] [INFO] Found 6/6 markers.
[2024-01-24 14:39:27,028] [INFO] Query marker FASTA was written to GCF_009604385.1_ASM960438v1_genomic.fna/markers.fasta
[2024-01-24 14:39:27,029] [INFO] Task started: Blastn
[2024-01-24 14:39:27,029] [INFO] Running command: blastn -query GCF_009604385.1_ASM960438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference/reference_markers.fasta -out GCF_009604385.1_ASM960438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:28,443] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:28,446] [INFO] Selected 27 target genomes.
[2024-01-24 14:39:28,446] [INFO] Target genome list was writen to GCF_009604385.1_ASM960438v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:28,459] [INFO] Task started: fastANI
[2024-01-24 14:39:28,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e30f61-bdfc-40b4-8bcd-1cf0e7805bae/GCF_009604385.1_ASM960438v1_genomic.fna.gz --refList GCF_009604385.1_ASM960438v1_genomic.fna/target_genomes.txt --output GCF_009604385.1_ASM960438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:16,773] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:16,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:16,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:16,793] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:16,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:16,794] [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 smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	100.0	2561	2564	95	conclusive
Streptomyces coryli	strain=A7024	GCA_011044975.1	1128680	1128680	type	True	80.8475	1225	2564	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	80.8089	769	2564	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	80.146	1182	2564	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	80.1386	1195	2564	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	80.0845	1190	2564	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	80.0791	1145	2564	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	80.077	927	2564	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.0708	1052	2564	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	80.0413	1201	2564	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	80.0278	1064	2564	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.0224	1157	2564	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	79.9459	1156	2564	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	79.8841	1102	2564	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	79.8248	1168	2564	95	below_threshold
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	79.765	1137	2564	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	79.7464	1169	2564	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	79.7385	1092	2564	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	79.719	1096	2564	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	79.706	1038	2564	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	79.6897	1160	2564	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	79.6799	1179	2564	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	79.6648	1180	2564	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	79.6597	1050	2564	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	79.6481	1223	2564	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	79.6359	1185	2564	95	below_threshold
Streptomyces bathyalis	strain=ASO4wet	GCA_015910445.1	2710756	2710756	type	True	79.1581	903	2564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,796] [INFO] DFAST Taxonomy check result was written to GCF_009604385.1_ASM960438v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:16,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:16,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:16,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference/checkm_data
[2024-01-24 14:40:16,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:16,868] [INFO] Task started: CheckM
[2024-01-24 14:40:16,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009604385.1_ASM960438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009604385.1_ASM960438v1_genomic.fna/checkm_input GCF_009604385.1_ASM960438v1_genomic.fna/checkm_result
[2024-01-24 14:41:25,298] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:25,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:25,322] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:25,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:25,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009604385.1_ASM960438v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:25,323] [INFO] Task started: Blastn
[2024-01-24 14:41:25,323] [INFO] Running command: blastn -query GCF_009604385.1_ASM960438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac64cbb3-5dc4-4be6-9802-a6184af05496/dqc_reference/reference_markers_gtdb.fasta -out GCF_009604385.1_ASM960438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:27,462] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:27,466] [INFO] Selected 27 target genomes.
[2024-01-24 14:41:27,466] [INFO] Target genome list was writen to GCF_009604385.1_ASM960438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:27,485] [INFO] Task started: fastANI
[2024-01-24 14:41:27,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e30f61-bdfc-40b4-8bcd-1cf0e7805bae/GCF_009604385.1_ASM960438v1_genomic.fna.gz --refList GCF_009604385.1_ASM960438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009604385.1_ASM960438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:17,072] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:17,093] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:17,093] [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_009604385.1	s__Streptomyces sp009604385	100.0	2561	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011044975.1	s__Streptomyces sp011044975	80.8425	1225	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847285.1	s__Streptomyces sp002847285	80.5764	1237	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
GCF_002797655.1	s__Streptomyces sp002797655	80.5199	1286	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
GCF_000514715.1	s__Streptomyces sp000514715	80.5015	1287	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482585.1	s__Streptomyces sp000482585	80.4202	1173	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	80.1792	1175	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_006782915.1	s__Streptomyces calvus	80.1573	1176	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	80.1435	1192	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCA_003719395.1	s__Streptomyces altiplanensis	80.1182	1019	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	96.26	0.83	0.83	2	-
GCF_014203535.1	s__Streptomyces griseostramineus	80.1084	1183	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_014649795.1	s__Streptomyces melanogenes	80.061	1150	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_014650335.1	s__Streptomyces hiroshimensis	80.0218	1064	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704425.1	s__Streptomyces fradiae	80.0214	1061	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	80.0061	1156	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	79.9945	1205	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_000716335.1	s__Streptomyces sp000716335	79.9882	1095	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004127445.1	s__Streptomyces alfalfae	79.8929	1101	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_001746415.1	s__Streptomyces agglomeratus	79.8899	1083	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_014596915.1	s__Streptomyces sp014596915	79.8621	1164	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704795.1	s__Streptomyces spectabilis	79.7047	1183	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	96.21	0.96	0.90	4	-
GCF_000716675.1	s__Streptomyces alboflavus	79.6978	1172	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_010384365.1	s__Streptomyces sp010384365	79.6967	1044	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
GCF_014650815.1	s__Streptomyces flavofungini	79.6931	1157	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002009175.1	s__Streptomyces niveus_A	79.5826	1055	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720475.1	s__Streptomyces aureocirculatus	79.5744	1069	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009755605.1	s__Streptomyces typhae	79.505	1138	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:17,096] [INFO] GTDB search result was written to GCF_009604385.1_ASM960438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:17,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:17,102] [INFO] DFAST_QC result json was written to GCF_009604385.1_ASM960438v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:17,103] [INFO] DFAST_QC completed!
[2024-01-24 14:42:17,103] [INFO] Total running time: 0h3m16s