[2024-01-24 13:55:17,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:17,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:17,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference
[2024-01-24 13:55:19,216] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:19,221] [INFO] Task started: Prodigal
[2024-01-24 13:55:19,222] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb1cff0c-26a2-4512-a265-0a1b8785c9ab/GCF_014650835.1_ASM1465083v1_genomic.fna.gz | prodigal -d GCF_014650835.1_ASM1465083v1_genomic.fna/cds.fna -a GCF_014650835.1_ASM1465083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:45,959] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:45,959] [INFO] Task started: HMMsearch
[2024-01-24 13:55:45,959] [INFO] Running command: hmmsearch --tblout GCF_014650835.1_ASM1465083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference/reference_markers.hmm GCF_014650835.1_ASM1465083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:46,408] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:46,409] [INFO] Found 6/6 markers.
[2024-01-24 13:55:46,482] [INFO] Query marker FASTA was written to GCF_014650835.1_ASM1465083v1_genomic.fna/markers.fasta
[2024-01-24 13:55:46,483] [INFO] Task started: Blastn
[2024-01-24 13:55:46,483] [INFO] Running command: blastn -query GCF_014650835.1_ASM1465083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference/reference_markers.fasta -out GCF_014650835.1_ASM1465083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:47,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:47,753] [INFO] Selected 18 target genomes.
[2024-01-24 13:55:47,753] [INFO] Target genome list was writen to GCF_014650835.1_ASM1465083v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:47,761] [INFO] Task started: fastANI
[2024-01-24 13:55:47,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1cff0c-26a2-4512-a265-0a1b8785c9ab/GCF_014650835.1_ASM1465083v1_genomic.fna.gz --refList GCF_014650835.1_ASM1465083v1_genomic.fna/target_genomes.txt --output GCF_014650835.1_ASM1465083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:29,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:29,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:29,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:29,122] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:56:29,123] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:56:29,123] [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 galilaeus	strain=JCM 4757	GCA_014650835.1	33899	33899	type	True	100.0	3054	3056	95	inconclusive
Streptomyces galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	99.9217	2541	3056	95	inconclusive
Streptomyces bobili	strain=NRRL B-1338	GCA_002154575.1	67280	67280	type	True	97.3935	2051	3056	95	inconclusive
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	86.6027	2115	3056	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	86.2174	2023	3056	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	86.2003	1964	3056	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	85.9342	1890	3056	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.1206	1990	3056	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.0999	1894	3056	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.9194	1790	3056	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	84.9082	1507	3056	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	84.8147	2023	3056	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	84.8037	1934	3056	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.7329	1715	3056	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.7183	1696	3056	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.444	1739	3056	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	83.9331	1835	3056	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	83.9123	1842	3056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:29,124] [INFO] DFAST Taxonomy check result was written to GCF_014650835.1_ASM1465083v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:29,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:29,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:29,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference/checkm_data
[2024-01-24 13:56:29,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:29,208] [INFO] Task started: CheckM
[2024-01-24 13:56:29,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650835.1_ASM1465083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650835.1_ASM1465083v1_genomic.fna/checkm_input GCF_014650835.1_ASM1465083v1_genomic.fna/checkm_result
[2024-01-24 13:58:33,826] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:33,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,856] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:33,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:33,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650835.1_ASM1465083v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:33,857] [INFO] Task started: Blastn
[2024-01-24 13:58:33,857] [INFO] Running command: blastn -query GCF_014650835.1_ASM1465083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d48b84a-2bde-4058-a473-18d8ec1389c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650835.1_ASM1465083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:35,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:35,864] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:35,864] [INFO] Target genome list was writen to GCF_014650835.1_ASM1465083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:36,213] [INFO] Task started: fastANI
[2024-01-24 13:58:36,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1cff0c-26a2-4512-a265-0a1b8785c9ab/GCF_014650835.1_ASM1465083v1_genomic.fna.gz --refList GCF_014650835.1_ASM1465083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650835.1_ASM1465083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:23,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:23,577] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:23,578] [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_002154575.1	s__Streptomyces bobili	97.3935	2051	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.61	97.61	0.88	0.85	3	conclusive
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	93.2606	2256	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	87.8826	2160	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129855.1	s__Streptomyces sp900129855	86.7938	1999	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_014648915.1	s__Streptomyces phaeofaciens	86.6061	2115	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110755.1	s__Streptomyces sp900110755	86.6044	1914	3056	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	86.3476	1915	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_001746365.1	s__Streptomyces sp001746365	86.0987	1937	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649655.1	s__Streptomyces humidus	85.9465	1889	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514285.1	s__Streptomyces sp001514285	85.9033	1923	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	85.4012	1991	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_000721105.1	s__Streptomyces cellulosae_A	85.2638	1895	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_000972385.1	s__Streptomyces sp000972385	85.1377	1853	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	85.0859	1898	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	84.8889	1641	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	84.806	1963	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746295.1	s__Streptomyces sp001746295	84.8033	2016	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513955.1	s__Streptomyces pseudovenezuelae	84.787	1938	3056	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	84.7565	1904	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383595.1	s__Streptomyces bottropensis	83.913	1841	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:23,580] [INFO] GTDB search result was written to GCF_014650835.1_ASM1465083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:23,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:23,585] [INFO] DFAST_QC result json was written to GCF_014650835.1_ASM1465083v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:23,585] [INFO] DFAST_QC completed!
[2024-01-24 13:59:23,585] [INFO] Total running time: 0h4m6s