[2024-01-25 17:53:05,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:05,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:05,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference
[2024-01-25 17:53:06,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:06,742] [INFO] Task started: Prodigal
[2024-01-25 17:53:06,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e0a5e3e-a0ba-4578-aab7-b6f9f10eb4f8/GCF_028401765.1_ASM2840176v1_genomic.fna.gz | prodigal -d GCF_028401765.1_ASM2840176v1_genomic.fna/cds.fna -a GCF_028401765.1_ASM2840176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:31,556] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:31,556] [INFO] Task started: HMMsearch
[2024-01-25 17:53:31,556] [INFO] Running command: hmmsearch --tblout GCF_028401765.1_ASM2840176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference/reference_markers.hmm GCF_028401765.1_ASM2840176v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:31,915] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:31,916] [INFO] Found 6/6 markers.
[2024-01-25 17:53:31,986] [INFO] Query marker FASTA was written to GCF_028401765.1_ASM2840176v1_genomic.fna/markers.fasta
[2024-01-25 17:53:31,986] [INFO] Task started: Blastn
[2024-01-25 17:53:31,987] [INFO] Running command: blastn -query GCF_028401765.1_ASM2840176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference/reference_markers.fasta -out GCF_028401765.1_ASM2840176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:33,245] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:33,249] [INFO] Selected 26 target genomes.
[2024-01-25 17:53:33,250] [INFO] Target genome list was writen to GCF_028401765.1_ASM2840176v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:33,273] [INFO] Task started: fastANI
[2024-01-25 17:53:33,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e0a5e3e-a0ba-4578-aab7-b6f9f10eb4f8/GCF_028401765.1_ASM2840176v1_genomic.fna.gz --refList GCF_028401765.1_ASM2840176v1_genomic.fna/target_genomes.txt --output GCF_028401765.1_ASM2840176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:36,842] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:36,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:36,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:36,859] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:54:36,859] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:54:36,860] [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 panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	93.8735	2555	3260	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	87.262	2010	3260	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.3331	2193	3260	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	86.0717	1963	3260	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	85.9843	2088	3260	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	85.9791	2204	3260	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.8753	1996	3260	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	85.8052	2191	3260	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.764	2018	3260	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	85.6852	2107	3260	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	85.6012	2117	3260	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	85.5293	2060	3260	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	85.4627	1971	3260	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.4592	1626	3260	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.3997	1781	3260	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	85.3366	1997	3260	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.2722	1866	3260	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	85.263	2126	3260	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	85.2421	1843	3260	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	85.192	1808	3260	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	85.1385	1826	3260	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.0273	1890	3260	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	84.9337	1896	3260	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.8878	1443	3260	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	84.0337	1586	3260	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	84.0056	1573	3260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:36,862] [INFO] DFAST Taxonomy check result was written to GCF_028401765.1_ASM2840176v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:36,863] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:36,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:36,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference/checkm_data
[2024-01-25 17:54:36,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:36,955] [INFO] Task started: CheckM
[2024-01-25 17:54:36,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028401765.1_ASM2840176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028401765.1_ASM2840176v1_genomic.fna/checkm_input GCF_028401765.1_ASM2840176v1_genomic.fna/checkm_result
[2024-01-25 17:56:56,648] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:56,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:56,677] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:56,677] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:56,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028401765.1_ASM2840176v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:56,678] [INFO] Task started: Blastn
[2024-01-25 17:56:56,678] [INFO] Running command: blastn -query GCF_028401765.1_ASM2840176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e7a64b-a2e5-400f-8ac5-4db7cdc9c103/dqc_reference/reference_markers_gtdb.fasta -out GCF_028401765.1_ASM2840176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:58,781] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:58,784] [INFO] Selected 17 target genomes.
[2024-01-25 17:56:58,784] [INFO] Target genome list was writen to GCF_028401765.1_ASM2840176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:58,797] [INFO] Task started: fastANI
[2024-01-25 17:56:58,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e0a5e3e-a0ba-4578-aab7-b6f9f10eb4f8/GCF_028401765.1_ASM2840176v1_genomic.fna.gz --refList GCF_028401765.1_ASM2840176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028401765.1_ASM2840176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:57:42,804] [INFO] Task succeeded: fastANI
[2024-01-25 17:57:42,815] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:57:42,815] [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_006715395.1	s__Streptomyces sp006715395	95.4024	2656	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	conclusive
GCF_001484565.1	s__Streptomyces sp001484565	93.7468	2719	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343515.1	s__Streptomyces sp004343515	88.2564	2328	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_000720765.1	s__Streptomyces sp000720765	87.8889	2264	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_003384795.1	s__Streptomyces sp003384795	87.6396	2181	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	87.5812	2260	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	86.3534	2184	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	86.218	2149	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	85.9738	2090	3260	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	85.8856	1994	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	85.868	2004	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	85.7795	2068	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_001514235.1	s__Streptomyces caeruleatus	85.7679	2016	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	85.5925	1961	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655715.1	s__Streptomyces lanatus	85.5118	2063	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857135.1	s__Streptomyces sp009857135	84.2316	1750	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419765.1	s__Streptomyces torulosus	84.051	1582	3260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:57:42,816] [INFO] GTDB search result was written to GCF_028401765.1_ASM2840176v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:57:42,817] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:57:42,820] [INFO] DFAST_QC result json was written to GCF_028401765.1_ASM2840176v1_genomic.fna/dqc_result.json
[2024-01-25 17:57:42,820] [INFO] DFAST_QC completed!
[2024-01-25 17:57:42,821] [INFO] Total running time: 0h4m37s