[2024-01-24 13:31:33,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference
[2024-01-24 13:31:34,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,803] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg437d229b-7386-4a73-bd5c-0b4fc25a48fa/GCF_001685355.1_ASM168535v1_genomic.fna.gz | prodigal -d GCF_001685355.1_ASM168535v1_genomic.fna/cds.fna -a GCF_001685355.1_ASM168535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:04,404] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:04,404] [INFO] Task started: HMMsearch
[2024-01-24 13:32:04,404] [INFO] Running command: hmmsearch --tblout GCF_001685355.1_ASM168535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference/reference_markers.hmm GCF_001685355.1_ASM168535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:04,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:04,839] [INFO] Found 6/6 markers.
[2024-01-24 13:32:04,933] [INFO] Query marker FASTA was written to GCF_001685355.1_ASM168535v1_genomic.fna/markers.fasta
[2024-01-24 13:32:04,934] [INFO] Task started: Blastn
[2024-01-24 13:32:04,934] [INFO] Running command: blastn -query GCF_001685355.1_ASM168535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference/reference_markers.fasta -out GCF_001685355.1_ASM168535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,281] [INFO] Selected 31 target genomes.
[2024-01-24 13:32:06,281] [INFO] Target genome list was writen to GCF_001685355.1_ASM168535v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,293] [INFO] Task started: fastANI
[2024-01-24 13:32:06,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg437d229b-7386-4a73-bd5c-0b4fc25a48fa/GCF_001685355.1_ASM168535v1_genomic.fna.gz --refList GCF_001685355.1_ASM168535v1_genomic.fna/target_genomes.txt --output GCF_001685355.1_ASM168535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:22,826] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:22,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:22,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:22,850] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:22,850] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:22,851] [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 resistomycificus	strain=NRRL 2290	GCA_001270505.1	67356	67356	type	True	87.5158	2201	3439	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	87.4378	2247	3439	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	87.4362	2260	3439	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	86.8749	2230	3439	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	86.8708	2398	3439	95	below_threshold
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	86.4634	2267	3439	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.3506	2136	3439	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.3487	2295	3439	95	below_threshold
Streptomyces antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	86.2715	2165	3439	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.2118	2078	3439	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	86.1745	2242	3439	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	86.0963	2177	3439	95	below_threshold
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	85.8914	2182	3439	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	85.8686	2196	3439	95	below_threshold
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	85.8585	2185	3439	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.8329	1860	3439	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.6829	1969	3439	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.6686	1868	3439	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	85.6618	2014	3439	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	85.5491	1957	3439	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	85.5469	1995	3439	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	85.205	2063	3439	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.097	1804	3439	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.0844	1829	3439	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	85.069	2111	3439	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.0605	1836	3439	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	84.876	1803	3439	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	84.2505	1959	3439	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	84.2217	1998	3439	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	84.1838	1986	3439	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	84.1277	1951	3439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:22,853] [INFO] DFAST Taxonomy check result was written to GCF_001685355.1_ASM168535v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:22,853] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:22,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:22,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference/checkm_data
[2024-01-24 13:33:22,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:22,956] [INFO] Task started: CheckM
[2024-01-24 13:33:22,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001685355.1_ASM168535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001685355.1_ASM168535v1_genomic.fna/checkm_input GCF_001685355.1_ASM168535v1_genomic.fna/checkm_result
[2024-01-24 13:36:32,137] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:32,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:32,168] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:32,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:32,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001685355.1_ASM168535v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:32,169] [INFO] Task started: Blastn
[2024-01-24 13:36:32,170] [INFO] Running command: blastn -query GCF_001685355.1_ASM168535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c094c93-45a5-4049-894b-7e355729655c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001685355.1_ASM168535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:34,148] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:34,169] [INFO] Selected 25 target genomes.
[2024-01-24 13:36:34,169] [INFO] Target genome list was writen to GCF_001685355.1_ASM168535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:34,262] [INFO] Task started: fastANI
[2024-01-24 13:36:34,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg437d229b-7386-4a73-bd5c-0b4fc25a48fa/GCF_001685355.1_ASM168535v1_genomic.fna.gz --refList GCF_001685355.1_ASM168535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001685355.1_ASM168535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:38,686] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:38,706] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:38,707] [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_001685355.1	s__Streptomyces lincolnensis	100.0	3433	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	conclusive
GCF_002291145.1	s__Streptomyces sp002291145	87.5212	2230	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279775.1	s__Streptomyces sp001279775	87.5121	2317	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514265.1	s__Streptomyces resistomycificus	87.4394	2261	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	87.3426	2333	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851625.1	s__Streptomyces sp003851625	87.2754	2318	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721105.1	s__Streptomyces cellulosae_A	87.2238	2197	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_001513955.1	s__Streptomyces pseudovenezuelae	86.8697	2231	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514145.1	s__Streptomyces canus	86.857	2401	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.82	96.31	0.85	0.84	3	-
GCF_003443735.1	s__Streptomyces sviceus	86.8241	2260	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0589	99.86	99.86	0.99	0.99	3	-
GCF_001282115.1	s__Streptomyces sp001282115	86.8104	1899	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_010548375.1	s__Streptomyces sp010548375	86.7675	2288	3439	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	86.6235	2319	3439	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	86.438	1860	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_003955715.1	s__Streptomyces aquilus	86.4296	2273	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	97.56	95.79	0.89	0.84	3	-
GCF_001514305.1	s__Streptomyces dysideae	86.3787	2133	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163075.1	s__Streptomyces sp015163075	86.3173	2302	3439	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	86.259	2236	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	86.1298	2002	3439	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	85.8473	2151	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648915.1	s__Streptomyces phaeofaciens	85.221	2060	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718785.1	s__Streptomyces sp000718785	84.5035	1757	3439	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	84.2351	1992	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	84.1765	1987	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386495.1	s__Streptomyces tailanensis	84.1544	1948	3439	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 13:37:38,708] [INFO] GTDB search result was written to GCF_001685355.1_ASM168535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:38,709] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:38,714] [INFO] DFAST_QC result json was written to GCF_001685355.1_ASM168535v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:38,715] [INFO] DFAST_QC completed!
[2024-01-24 13:37:38,715] [INFO] Total running time: 0h6m5s