[2024-01-24 11:20:49,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,944] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference
[2024-01-24 11:20:51,158] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,159] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg931349f4-54b8-4b8e-b9d2-2ccd5411bb66/GCF_002154375.1_ASM215437v1_genomic.fna.gz | prodigal -d GCF_002154375.1_ASM215437v1_genomic.fna/cds.fna -a GCF_002154375.1_ASM215437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:10,721] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:10,721] [INFO] Task started: HMMsearch
[2024-01-24 11:21:10,721] [INFO] Running command: hmmsearch --tblout GCF_002154375.1_ASM215437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference/reference_markers.hmm GCF_002154375.1_ASM215437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:11,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:11,085] [INFO] Found 6/6 markers.
[2024-01-24 11:21:11,153] [INFO] Query marker FASTA was written to GCF_002154375.1_ASM215437v1_genomic.fna/markers.fasta
[2024-01-24 11:21:11,154] [INFO] Task started: Blastn
[2024-01-24 11:21:11,154] [INFO] Running command: blastn -query GCF_002154375.1_ASM215437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference/reference_markers.fasta -out GCF_002154375.1_ASM215437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:12,496] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:12,499] [INFO] Selected 32 target genomes.
[2024-01-24 11:21:12,499] [INFO] Target genome list was writen to GCF_002154375.1_ASM215437v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:12,512] [INFO] Task started: fastANI
[2024-01-24 11:21:12,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg931349f4-54b8-4b8e-b9d2-2ccd5411bb66/GCF_002154375.1_ASM215437v1_genomic.fna.gz --refList GCF_002154375.1_ASM215437v1_genomic.fna/target_genomes.txt --output GCF_002154375.1_ASM215437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:22:05,915] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:05,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:22:05,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:22:05,940] [INFO] Found 32 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:22:05,940] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:22:05,941] [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 glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	100.0	2264	2304	95	conclusive
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	86.3391	1416	2304	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	86.2893	1503	2304	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	86.2555	1529	2304	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	86.1848	1445	2304	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.9904	1539	2304	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.8724	1548	2304	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.8374	1522	2304	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.8328	1546	2304	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.828	1351	2304	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	85.6604	1512	2304	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	85.5471	1523	2304	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	85.5275	1519	2304	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	85.5247	1513	2304	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	85.4086	1405	2304	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	85.407	1387	2304	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	85.4017	1438	2304	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.3401	1506	2304	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	85.3343	1458	2304	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	85.3203	1481	2304	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.1017	1282	2304	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.0727	1347	2304	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	85.0499	1512	2304	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	84.9042	1473	2304	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	84.9022	1363	2304	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.852	1368	2304	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.1921	1185	2304	95	below_threshold
Streptomyces xantholiticus	strain=JCM 4863	GCA_014651015.1	68285	68285	type	True	81.6576	1161	2304	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	76.446	119	2304	95	below_threshold
Aestuariimicrobium kwangyangense	strain=DSM 21549	GCA_000421525.1	396389	396389	type	True	76.4348	166	2304	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	76.2339	239	2304	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	76.0455	354	2304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:22:05,942] [INFO] DFAST Taxonomy check result was written to GCF_002154375.1_ASM215437v1_genomic.fna/tc_result.tsv
[2024-01-24 11:22:05,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:22:05,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:22:05,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference/checkm_data
[2024-01-24 11:22:05,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:22:06,024] [INFO] Task started: CheckM
[2024-01-24 11:22:06,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154375.1_ASM215437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154375.1_ASM215437v1_genomic.fna/checkm_input GCF_002154375.1_ASM215437v1_genomic.fna/checkm_result
[2024-01-24 11:23:34,743] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:34,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:34,772] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:34,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:34,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154375.1_ASM215437v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:34,773] [INFO] Task started: Blastn
[2024-01-24 11:23:34,773] [INFO] Running command: blastn -query GCF_002154375.1_ASM215437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7a3f585-94cf-43e9-900c-935b367dc7a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154375.1_ASM215437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:36,969] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:36,972] [INFO] Selected 21 target genomes.
[2024-01-24 11:23:36,972] [INFO] Target genome list was writen to GCF_002154375.1_ASM215437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:37,012] [INFO] Task started: fastANI
[2024-01-24 11:23:37,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg931349f4-54b8-4b8e-b9d2-2ccd5411bb66/GCF_002154375.1_ASM215437v1_genomic.fna.gz --refList GCF_002154375.1_ASM215437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154375.1_ASM215437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:15,454] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:15,474] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:15,474] [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_002128465.1	s__Streptomyces pharetrae	97.5128	1888	2304	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_000761215.1	s__Streptomyces glaucescens	93.9507	1856	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	90.0799	1669	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	89.6956	1691	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	86.3195	1537	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	86.2887	1503	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_014656055.1	s__Streptomyces griseosporeus	85.9891	1538	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	85.5158	1515	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002027195.1	s__Streptomyces sp002027195	85.4774	1351	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	85.3676	1453	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_019049325.1	s__Streptomyces sp019049325	85.1663	1395	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509795.1	s__Streptomyces sp001509795	85.1356	1411	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_000725125.1	s__Streptomyces toyocaensis	85.0793	1377	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	85.0654	1527	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649355.1	s__Streptomyces althioticus	84.9873	1415	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCF_007176755.1	s__Streptomyces sp007176755	84.939	1441	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	84.8857	1490	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651015.1	s__Streptomyces xantholiticus	81.6766	1158	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.93	95.93	0.86	0.86	2	-
GCF_001905795.1	s__Streptomyces sp001905795	81.4297	1081	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287935.1	s__Streptomyces sp003287935	81.0045	1162	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.55	99.55	0.95	0.95	2	-
GCF_000424845.1	s__Streptomyces sp000424845	79.8103	789	2304	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 11:24:15,476] [INFO] GTDB search result was written to GCF_002154375.1_ASM215437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:15,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:15,481] [INFO] DFAST_QC result json was written to GCF_002154375.1_ASM215437v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:15,482] [INFO] DFAST_QC completed!
[2024-01-24 11:24:15,482] [INFO] Total running time: 0h3m26s