[2024-01-24 11:58:55,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference
[2024-01-24 11:58:56,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:56,501] [INFO] Task started: Prodigal
[2024-01-24 11:58:56,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a50d0f1-2cbd-4ea6-856f-04ab7bb4c334/GCF_021261325.1_ASM2126132v1_genomic.fna.gz | prodigal -d GCF_021261325.1_ASM2126132v1_genomic.fna/cds.fna -a GCF_021261325.1_ASM2126132v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:26,899] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:26,899] [INFO] Task started: HMMsearch
[2024-01-24 11:59:26,899] [INFO] Running command: hmmsearch --tblout GCF_021261325.1_ASM2126132v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference/reference_markers.hmm GCF_021261325.1_ASM2126132v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:27,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:27,413] [INFO] Found 6/6 markers.
[2024-01-24 11:59:27,491] [INFO] Query marker FASTA was written to GCF_021261325.1_ASM2126132v1_genomic.fna/markers.fasta
[2024-01-24 11:59:27,491] [INFO] Task started: Blastn
[2024-01-24 11:59:27,491] [INFO] Running command: blastn -query GCF_021261325.1_ASM2126132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference/reference_markers.fasta -out GCF_021261325.1_ASM2126132v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:28,845] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:28,849] [INFO] Selected 27 target genomes.
[2024-01-24 11:59:28,850] [INFO] Target genome list was writen to GCF_021261325.1_ASM2126132v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:28,859] [INFO] Task started: fastANI
[2024-01-24 11:59:28,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a50d0f1-2cbd-4ea6-856f-04ab7bb4c334/GCF_021261325.1_ASM2126132v1_genomic.fna.gz --refList GCF_021261325.1_ASM2126132v1_genomic.fna/target_genomes.txt --output GCF_021261325.1_ASM2126132v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:30,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:30,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:30,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:30,619] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:30,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:30,620] [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 plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	87.7969	2022	3457	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	87.3378	2104	3457	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.3276	2236	3457	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	86.2222	2010	3457	95	below_threshold
Streptomyces antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	86.0828	2118	3457	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.0365	2233	3457	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	85.9145	2302	3457	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	85.8763	2109	3457	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	85.8615	2254	3457	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.8595	2174	3457	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.81	2139	3457	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	85.7739	2118	3457	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.6523	1841	3457	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	85.3236	1971	3457	95	below_threshold
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	85.196	2013	3457	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.0239	1507	3457	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.9746	1846	3457	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	84.8625	1957	3457	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.8603	1693	3457	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.8308	1702	3457	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	84.65	1464	3457	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	84.6356	1944	3457	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	84.5952	1850	3457	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	84.5186	1948	3457	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	84.3523	1937	3457	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	83.9015	1917	3457	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	83.791	1980	3457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:30,621] [INFO] DFAST Taxonomy check result was written to GCF_021261325.1_ASM2126132v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:30,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:30,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:30,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference/checkm_data
[2024-01-24 12:00:30,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:30,716] [INFO] Task started: CheckM
[2024-01-24 12:00:30,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021261325.1_ASM2126132v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021261325.1_ASM2126132v1_genomic.fna/checkm_input GCF_021261325.1_ASM2126132v1_genomic.fna/checkm_result
[2024-01-24 12:02:58,342] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:58,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 12:02:58,367] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:58,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:58,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021261325.1_ASM2126132v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:58,368] [INFO] Task started: Blastn
[2024-01-24 12:02:58,368] [INFO] Running command: blastn -query GCF_021261325.1_ASM2126132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg245a70ab-3dd8-45ee-abc2-6d32a1e83118/dqc_reference/reference_markers_gtdb.fasta -out GCF_021261325.1_ASM2126132v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:03:00,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:03:00,315] [INFO] Selected 18 target genomes.
[2024-01-24 12:03:00,315] [INFO] Target genome list was writen to GCF_021261325.1_ASM2126132v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:03:00,325] [INFO] Task started: fastANI
[2024-01-24 12:03:00,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a50d0f1-2cbd-4ea6-856f-04ab7bb4c334/GCF_021261325.1_ASM2126132v1_genomic.fna.gz --refList GCF_021261325.1_ASM2126132v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021261325.1_ASM2126132v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:03:42,198] [INFO] Task succeeded: fastANI
[2024-01-24 12:03:42,212] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:03:42,213] [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_000720765.1	s__Streptomyces sp000720765	92.8021	2638	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_002754715.1	s__Streptomyces sp002754715	92.2085	2600	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384795.1	s__Streptomyces sp003384795	92.1868	2485	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411315.1	s__Streptomyces sp000411315	88.0248	2113	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104505.1	s__Streptomyces sp003046555	87.9729	2077	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.74	99.48	0.99	0.97	3	-
GCF_006715395.1	s__Streptomyces sp006715395	87.3144	2235	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_001484565.1	s__Streptomyces sp001484565	87.28	2233	3457	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	87.1972	2328	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_001514065.1	s__Streptomyces antibioticus	86.0668	2122	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	N/A	N/A	N/A	N/A	1	-
GCF_001514145.1	s__Streptomyces canus	85.9369	2297	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.82	96.31	0.85	0.84	3	-
GCF_001270495.1	s__Streptomyces viridochromogenes_A	85.9008	2153	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCF_001282115.1	s__Streptomyces sp001282115	85.8893	1813	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900103585.1	s__Streptomyces sp900103585	85.8035	2227	3457	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	85.7834	2144	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	84.7961	1748	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939385.1	s__Streptomyces sp002939385	84.6793	1619	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_004124325.1	s__Streptomyces sp004124325	84.6077	1746	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	84.4435	1636	3457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:03:42,214] [INFO] GTDB search result was written to GCF_021261325.1_ASM2126132v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:03:42,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:03:42,220] [INFO] DFAST_QC result json was written to GCF_021261325.1_ASM2126132v1_genomic.fna/dqc_result.json
[2024-01-24 12:03:42,220] [INFO] DFAST_QC completed!
[2024-01-24 12:03:42,220] [INFO] Total running time: 0h4m47s