[2024-01-24 12:07:06,742] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference
[2024-01-24 12:07:07,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,983] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg6622722f-61d1-4796-b22f-178b08737ce9/GCF_021390235.1_ASM2139023v1_genomic.fna.gz | prodigal -d GCF_021390235.1_ASM2139023v1_genomic.fna/cds.fna -a GCF_021390235.1_ASM2139023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:34,186] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:34,186] [INFO] Task started: HMMsearch
[2024-01-24 12:07:34,186] [INFO] Running command: hmmsearch --tblout GCF_021390235.1_ASM2139023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference/reference_markers.hmm GCF_021390235.1_ASM2139023v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:34,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:34,674] [INFO] Found 6/6 markers.
[2024-01-24 12:07:34,749] [INFO] Query marker FASTA was written to GCF_021390235.1_ASM2139023v1_genomic.fna/markers.fasta
[2024-01-24 12:07:34,750] [INFO] Task started: Blastn
[2024-01-24 12:07:34,750] [INFO] Running command: blastn -query GCF_021390235.1_ASM2139023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference/reference_markers.fasta -out GCF_021390235.1_ASM2139023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:36,052] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:36,056] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:36,056] [INFO] Target genome list was writen to GCF_021390235.1_ASM2139023v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:36,063] [INFO] Task started: fastANI
[2024-01-24 12:07:36,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg6622722f-61d1-4796-b22f-178b08737ce9/GCF_021390235.1_ASM2139023v1_genomic.fna.gz --refList GCF_021390235.1_ASM2139023v1_genomic.fna/target_genomes.txt --output GCF_021390235.1_ASM2139023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:10,038] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:10,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:10,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:10,063] [INFO] Found 16 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:08:10,063] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:08:10,063] [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 purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	100.0	3091	3095	95	inconclusive
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	99.9945	3090	3095	95	inconclusive
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	95.7297	2596	3095	95	inconclusive
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	95.694	2607	3095	95	inconclusive
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	95.5588	2580	3095	95	inconclusive
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.3546	2263	3095	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	90.7946	2363	3095	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	90.7302	2299	3095	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.3042	1810	3095	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	90.2034	2279	3095	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	89.9884	1936	3095	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.4602	1766	3095	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	84.2926	1604	3095	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.4949	1040	3095	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	78.3617	1023	3095	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.587	558	3095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:10,067] [INFO] DFAST Taxonomy check result was written to GCF_021390235.1_ASM2139023v1_genomic.fna/tc_result.tsv
[2024-01-24 12:08:10,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:10,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:10,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference/checkm_data
[2024-01-24 12:08:10,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:10,156] [INFO] Task started: CheckM
[2024-01-24 12:08:10,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021390235.1_ASM2139023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021390235.1_ASM2139023v1_genomic.fna/checkm_input GCF_021390235.1_ASM2139023v1_genomic.fna/checkm_result
[2024-01-24 12:10:17,760] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:17,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:17,791] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:17,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:17,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021390235.1_ASM2139023v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:17,792] [INFO] Task started: Blastn
[2024-01-24 12:10:17,792] [INFO] Running command: blastn -query GCF_021390235.1_ASM2139023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2d3a8eb-4310-4769-bc6b-2990f95fa638/dqc_reference/reference_markers_gtdb.fasta -out GCF_021390235.1_ASM2139023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:19,869] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:19,874] [INFO] Selected 25 target genomes.
[2024-01-24 12:10:19,874] [INFO] Target genome list was writen to GCF_021390235.1_ASM2139023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:19,905] [INFO] Task started: fastANI
[2024-01-24 12:10:19,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg6622722f-61d1-4796-b22f-178b08737ce9/GCF_021390235.1_ASM2139023v1_genomic.fna.gz --refList GCF_021390235.1_ASM2139023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021390235.1_ASM2139023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:11:14,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:11:14,315] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:11:14,315] [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_000715635.1	s__Streptomyces violaceus	95.1683	2558	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.39	95.19	0.85	0.83	5	conclusive
GCF_018604545.1	s__Streptomyces sp018604545	94.563	2514	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000415505.1	s__Streptomyces afghaniensis	91.5966	2204	3095	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	91.5623	2327	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCA_018195615.1	s__Streptomyces tuirus_A	91.2571	2265	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150735.1	s__Streptomyces africanus	91.2079	2027	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	91.0402	2273	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	90.8504	2292	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648995.1	s__Streptomyces massasporeus	90.799	2362	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCA_014204745.1	s__Streptomyces collinus	90.7558	2296	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_014205055.1	s__Streptomyces luteogriseus	90.5092	2263	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_000717875.1	s__Streptomyces sp000717875	90.4449	2092	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCF_014651075.1	s__Streptomyces djakartensis	90.2251	1990	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655005.1	s__Streptomyces tibetensis	90.225	2276	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004028635.1	s__Streptomyces cyaneus	86.156	2164	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	86.016	1850	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	85.9613	2131	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	85.8472	2051	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364215.1	s__Streptomyces sp004364215	85.7919	2057	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282115.1	s__Streptomyces sp001282115	85.6662	1732	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_003671715.1	s__Streptomyces sp003671715	85.6434	1814	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCA_003248315.1	s__Streptomyces sp003248315	85.4884	1733	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	85.2182	1793	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003143855.1	s__Streptomyces sp003143855	85.2105	1659	3095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCA_014649295.1	s__Streptomyces libani_A	84.4743	1705	3095	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 12:11:14,317] [INFO] GTDB search result was written to GCF_021390235.1_ASM2139023v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:11:14,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:11:14,322] [INFO] DFAST_QC result json was written to GCF_021390235.1_ASM2139023v1_genomic.fna/dqc_result.json
[2024-01-24 12:11:14,322] [INFO] DFAST_QC completed!
[2024-01-24 12:11:14,322] [INFO] Total running time: 0h4m8s