[2024-01-24 12:40:50,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,367] [INFO] DQC Reference Directory: /var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference
[2024-01-24 12:40:51,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,603] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a48543a-0f4b-4783-8293-eaf6be7bbf53/GCF_030551255.1_ASM3055125v1_genomic.fna.gz | prodigal -d GCF_030551255.1_ASM3055125v1_genomic.fna/cds.fna -a GCF_030551255.1_ASM3055125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:34,226] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:34,227] [INFO] Task started: HMMsearch
[2024-01-24 12:41:34,227] [INFO] Running command: hmmsearch --tblout GCF_030551255.1_ASM3055125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference/reference_markers.hmm GCF_030551255.1_ASM3055125v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:34,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:34,677] [INFO] Found 6/6 markers.
[2024-01-24 12:41:34,772] [INFO] Query marker FASTA was written to GCF_030551255.1_ASM3055125v1_genomic.fna/markers.fasta
[2024-01-24 12:41:34,773] [INFO] Task started: Blastn
[2024-01-24 12:41:34,773] [INFO] Running command: blastn -query GCF_030551255.1_ASM3055125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference/reference_markers.fasta -out GCF_030551255.1_ASM3055125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:36,048] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:36,052] [INFO] Selected 27 target genomes.
[2024-01-24 12:41:36,052] [INFO] Target genome list was writen to GCF_030551255.1_ASM3055125v1_genomic.fna/target_genomes.txt
[2024-01-24 12:41:36,075] [INFO] Task started: fastANI
[2024-01-24 12:41:36,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a48543a-0f4b-4783-8293-eaf6be7bbf53/GCF_030551255.1_ASM3055125v1_genomic.fna.gz --refList GCF_030551255.1_ASM3055125v1_genomic.fna/target_genomes.txt --output GCF_030551255.1_ASM3055125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:42,962] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:42,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:42,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:42,985] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:42:42,986] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:42:42,986] [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 dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.8781	2249	4130	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	86.7347	2057	4130	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.5614	2241	4130	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.3709	2132	4130	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	86.3331	2141	4130	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	86.3142	2272	4130	95	below_threshold
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	86.2538	2240	4130	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	86.1153	2191	4130	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	86.1133	2226	4130	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	86.0672	2213	4130	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.0445	1967	4130	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	85.9334	1910	4130	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	85.9227	2019	4130	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	85.8917	2086	4130	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.8223	2184	4130	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.7212	2218	4130	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.2747	1951	4130	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	85.0106	1824	4130	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	84.9844	1840	4130	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	84.932	1498	4130	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.9097	1922	4130	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.8773	1796	4130	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	84.8634	1792	4130	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	84.8101	2149	4130	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	84.7701	1851	4130	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.7262	1547	4130	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	84.543	1765	4130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:42,988] [INFO] DFAST Taxonomy check result was written to GCF_030551255.1_ASM3055125v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:42,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:42,989] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:42,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference/checkm_data
[2024-01-24 12:42:42,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:43,097] [INFO] Task started: CheckM
[2024-01-24 12:42:43,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030551255.1_ASM3055125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030551255.1_ASM3055125v1_genomic.fna/checkm_input GCF_030551255.1_ASM3055125v1_genomic.fna/checkm_result
[2024-01-24 12:45:51,255] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:51,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-24 12:45:51,285] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:51,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:51,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030551255.1_ASM3055125v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:51,286] [INFO] Task started: Blastn
[2024-01-24 12:45:51,286] [INFO] Running command: blastn -query GCF_030551255.1_ASM3055125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7f64aed-0158-4e94-9fec-5170bedcf673/dqc_reference/reference_markers_gtdb.fasta -out GCF_030551255.1_ASM3055125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:53,377] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:53,381] [INFO] Selected 19 target genomes.
[2024-01-24 12:45:53,381] [INFO] Target genome list was writen to GCF_030551255.1_ASM3055125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:53,400] [INFO] Task started: fastANI
[2024-01-24 12:45:53,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a48543a-0f4b-4783-8293-eaf6be7bbf53/GCF_030551255.1_ASM3055125v1_genomic.fna.gz --refList GCF_030551255.1_ASM3055125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030551255.1_ASM3055125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:49,021] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:49,041] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:49,041] [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_003851625.1	s__Streptomyces sp003851625	99.9252	3875	4130	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_002291145.1	s__Streptomyces sp002291145	92.7853	2550	4130	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	88.2434	2369	4130	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	87.99	2339	4130	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	87.4979	2292	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_000720805.1	s__Streptomyces violaceoruber_B	87.3801	2272	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	87.239	2375	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_004028635.1	s__Streptomyces cyaneus	86.5549	2242	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827025.1	s__Streptomyces sp009827025	86.3168	1883	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.69	97.69	0.89	0.89	2	-
GCF_014651035.1	s__Streptomyces lomondensis	86.3155	2145	4130	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	86.3139	2079	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948485.1	s__Streptomyces sp017948485	86.019	2217	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	85.924	1999	4130	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	85.7804	2140	4130	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	85.7251	2215	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720255.1	s__Streptomyces griseus_I	85.7149	2172	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267885.1	s__Streptomyces ambofaciens	84.8081	1850	4130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_018070565.1	s__Streptomyces sp018070565	84.8014	1840	4130	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	84.4034	1792	4130	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 12:46:49,043] [INFO] GTDB search result was written to GCF_030551255.1_ASM3055125v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:49,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:49,048] [INFO] DFAST_QC result json was written to GCF_030551255.1_ASM3055125v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:49,049] [INFO] DFAST_QC completed!
[2024-01-24 12:46:49,049] [INFO] Total running time: 0h5m59s