[2024-01-25 20:01:35,466] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:35,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:35,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference
[2024-01-25 20:01:36,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:36,577] [INFO] Task started: Prodigal
[2024-01-25 20:01:36,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg41470d1e-2c35-4246-9a4c-75cc00da44d5/GCF_014650555.1_ASM1465055v1_genomic.fna.gz | prodigal -d GCF_014650555.1_ASM1465055v1_genomic.fna/cds.fna -a GCF_014650555.1_ASM1465055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:58,445] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:58,446] [INFO] Task started: HMMsearch
[2024-01-25 20:01:58,446] [INFO] Running command: hmmsearch --tblout GCF_014650555.1_ASM1465055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference/reference_markers.hmm GCF_014650555.1_ASM1465055v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:58,753] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:58,754] [INFO] Found 6/6 markers.
[2024-01-25 20:01:58,814] [INFO] Query marker FASTA was written to GCF_014650555.1_ASM1465055v1_genomic.fna/markers.fasta
[2024-01-25 20:01:58,814] [INFO] Task started: Blastn
[2024-01-25 20:01:58,814] [INFO] Running command: blastn -query GCF_014650555.1_ASM1465055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference/reference_markers.fasta -out GCF_014650555.1_ASM1465055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:00,077] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:00,080] [INFO] Selected 27 target genomes.
[2024-01-25 20:02:00,081] [INFO] Target genome list was writen to GCF_014650555.1_ASM1465055v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:00,096] [INFO] Task started: fastANI
[2024-01-25 20:02:00,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg41470d1e-2c35-4246-9a4c-75cc00da44d5/GCF_014650555.1_ASM1465055v1_genomic.fna.gz --refList GCF_014650555.1_ASM1465055v1_genomic.fna/target_genomes.txt --output GCF_014650555.1_ASM1465055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:49,686] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:49,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:49,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:49,704] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:49,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:49,704] [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 goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	100.0	2770	2773	95	conclusive
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	88.0771	1820	2773	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	87.8954	1843	2773	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	87.6582	1926	2773	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	87.6329	1924	2773	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	87.6199	1926	2773	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	87.5373	1873	2773	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	87.3946	1834	2773	95	below_threshold
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	87.3454	1816	2773	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	87.3385	1834	2773	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	87.3118	1858	2773	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	87.1081	1734	2773	95	below_threshold
Streptomyces cirratus	strain=JCM 4738	GCA_014650775.1	68187	68187	type	True	87.0728	1707	2773	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	87.0709	1828	2773	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	87.0564	1719	2773	95	below_threshold
Streptomyces katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	87.0542	1323	2773	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	86.9236	1716	2773	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.7337	1036	2773	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.6683	1048	2773	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.5353	1373	2773	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.1596	1311	2773	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.1035	1211	2773	95	below_threshold
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	80.7305	886	2773	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	76.5331	649	2773	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	76.5313	642	2773	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	76.4971	775	2773	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	76.4534	712	2773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:49,706] [INFO] DFAST Taxonomy check result was written to GCF_014650555.1_ASM1465055v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:49,707] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:49,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:49,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference/checkm_data
[2024-01-25 20:02:49,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:49,788] [INFO] Task started: CheckM
[2024-01-25 20:02:49,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650555.1_ASM1465055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650555.1_ASM1465055v1_genomic.fna/checkm_input GCF_014650555.1_ASM1465055v1_genomic.fna/checkm_result
[2024-01-25 20:04:15,936] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:15,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:15,958] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:15,958] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:15,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650555.1_ASM1465055v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:15,959] [INFO] Task started: Blastn
[2024-01-25 20:04:15,959] [INFO] Running command: blastn -query GCF_014650555.1_ASM1465055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875cc98d-64ff-42b5-ade9-6cb3055eb57c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650555.1_ASM1465055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:18,053] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:18,056] [INFO] Selected 23 target genomes.
[2024-01-25 20:04:18,056] [INFO] Target genome list was writen to GCF_014650555.1_ASM1465055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:18,109] [INFO] Task started: fastANI
[2024-01-25 20:04:18,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg41470d1e-2c35-4246-9a4c-75cc00da44d5/GCF_014650555.1_ASM1465055v1_genomic.fna.gz --refList GCF_014650555.1_ASM1465055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650555.1_ASM1465055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:06,266] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:06,280] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:06,280] [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_014650555.1	s__Streptomyces goshikiensis	100.0	2770	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	conclusive
GCF_018614095.1	s__Streptomyces sp018614095	88.8175	1727	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.34	0.93	0.89	3	-
GCF_000717915.1	s__Streptomyces sp000717915	88.5005	1770	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_008704935.1	s__Streptomyces vinaceus	88.0562	1823	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	97.63	0.95	0.92	5	-
GCF_018614075.1	s__Streptomyces sp018614075	87.9986	1601	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717655.1	s__Streptomyces katrae_B	87.8762	1856	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.60	96.50	0.86	0.86	4	-
GCF_017639205.1	s__Streptomyces nojiriensis	87.6615	1924	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000720115.1	s__Streptomyces sp000720115	87.6219	1790	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044425.1	s__Streptomyces roseus	87.5988	1805	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016755875.1	s__Streptomyces spororaveus	87.5248	1875	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725555.1	s__Streptomyces erythrochromogenes	87.4867	1697	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.80	95.80	0.85	0.85	2	-
GCF_002080455.1	s__Streptomyces sp002080455	87.483	1863	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCA_001298555.1	s__Streptomyces sp001298555	87.3994	1798	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650695.1	s__Streptomyces avidinii	87.3456	1834	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000716685.1	s__Streptomyces virginiae_A	87.232	1908	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_002803845.1	s__Streptomyces lavendulae_C	87.1055	1912	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_001941845.1	s__Streptomyces sp001941845	87.0276	1681	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.45	99.45	0.96	0.96	2	-
GCF_001953875.1	s__Streptomyces amritsarensis	86.983	1708	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	98.97	0.95	0.93	4	-
GCF_003287935.1	s__Streptomyces sp003287935	86.8359	1782	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.55	99.55	0.95	0.95	2	-
GCF_005981925.1	s__Streptomyces albidochromogenes	82.2307	1213	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	-
GCF_001905905.1	s__Streptomyces sp001905905	81.7138	1308	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_900091725.1	s__Streptomyces sp900091725	81.6226	1358	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007829855.1	s__Streptomyces argenteolus	81.3189	1280	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:06,282] [INFO] GTDB search result was written to GCF_014650555.1_ASM1465055v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:06,283] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:06,286] [INFO] DFAST_QC result json was written to GCF_014650555.1_ASM1465055v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:06,287] [INFO] DFAST_QC completed!
[2024-01-25 20:05:06,287] [INFO] Total running time: 0h3m31s