[2024-01-24 14:19:44,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:44,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:44,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference
[2024-01-24 14:19:46,051] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:46,052] [INFO] Task started: Prodigal
[2024-01-24 14:19:46,052] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e714a4e-f65a-434a-83f5-8805e931a12d/GCF_020400685.1_ASM2040068v1_genomic.fna.gz | prodigal -d GCF_020400685.1_ASM2040068v1_genomic.fna/cds.fna -a GCF_020400685.1_ASM2040068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:16,002] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:16,002] [INFO] Task started: HMMsearch
[2024-01-24 14:20:16,002] [INFO] Running command: hmmsearch --tblout GCF_020400685.1_ASM2040068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference/reference_markers.hmm GCF_020400685.1_ASM2040068v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:16,497] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:16,499] [INFO] Found 6/6 markers.
[2024-01-24 14:20:16,578] [INFO] Query marker FASTA was written to GCF_020400685.1_ASM2040068v1_genomic.fna/markers.fasta
[2024-01-24 14:20:16,578] [INFO] Task started: Blastn
[2024-01-24 14:20:16,578] [INFO] Running command: blastn -query GCF_020400685.1_ASM2040068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference/reference_markers.fasta -out GCF_020400685.1_ASM2040068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,047] [INFO] Selected 25 target genomes.
[2024-01-24 14:20:18,047] [INFO] Target genome list was writen to GCF_020400685.1_ASM2040068v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:18,098] [INFO] Task started: fastANI
[2024-01-24 14:20:18,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e714a4e-f65a-434a-83f5-8805e931a12d/GCF_020400685.1_ASM2040068v1_genomic.fna.gz --refList GCF_020400685.1_ASM2040068v1_genomic.fna/target_genomes.txt --output GCF_020400685.1_ASM2040068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:21:11,142] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:11,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:21:11,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:21:11,165] [INFO] Found 25 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:21:11,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:21:11,166] [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 echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	100.0	3020	3023	95	conclusive
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	99.998	3014	3023	95	conclusive
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	92.7821	2420	3023	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	89.7937	2081	3023	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	89.7676	2072	3023	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	89.7429	2093	3023	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	89.5468	2052	3023	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	89.1879	1964	3023	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	89.1323	1932	3023	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.0993	1895	3023	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.0999	1973	3023	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	88.0936	2070	3023	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	87.497	2008	3023	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	87.4046	1962	3023	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.1274	1573	3023	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.7601	1737	3023	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	84.7407	1688	3023	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.5206	1416	3023	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.6019	1165	3023	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	79.9857	875	3023	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.7179	1164	3023	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	79.6284	1250	3023	95	below_threshold
Streptomyces bathyalis	strain=ASO4wet	GCA_015910445.1	2710756	2710756	type	True	79.3222	989	3023	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.2409	962	3023	95	below_threshold
Tsukamurella spumae	strain=DSM 44113	GCA_012396015.1	44753	44753	type	True	76.0947	368	3023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:21:11,167] [INFO] DFAST Taxonomy check result was written to GCF_020400685.1_ASM2040068v1_genomic.fna/tc_result.tsv
[2024-01-24 14:21:11,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:21:11,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:21:11,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference/checkm_data
[2024-01-24 14:21:11,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:21:11,329] [INFO] Task started: CheckM
[2024-01-24 14:21:11,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020400685.1_ASM2040068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020400685.1_ASM2040068v1_genomic.fna/checkm_input GCF_020400685.1_ASM2040068v1_genomic.fna/checkm_result
[2024-01-24 14:23:21,875] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:21,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:21,903] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:21,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:21,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020400685.1_ASM2040068v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:21,904] [INFO] Task started: Blastn
[2024-01-24 14:23:21,904] [INFO] Running command: blastn -query GCF_020400685.1_ASM2040068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg201de21f-d086-4059-b28d-eb6d6447003b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020400685.1_ASM2040068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:24,331] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:24,335] [INFO] Selected 25 target genomes.
[2024-01-24 14:23:24,335] [INFO] Target genome list was writen to GCF_020400685.1_ASM2040068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:24,367] [INFO] Task started: fastANI
[2024-01-24 14:23:24,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e714a4e-f65a-434a-83f5-8805e931a12d/GCF_020400685.1_ASM2040068v1_genomic.fna.gz --refList GCF_020400685.1_ASM2040068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020400685.1_ASM2040068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:24,464] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:24,483] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:24,484] [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_014203595.1	s__Streptomyces echinatus	99.998	3014	3023	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_016741855.1	s__Streptomyces musisoli	92.7854	2419	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	90.004	1674	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_017526105.1	s__Streptomyces cyanogenus	89.9499	2091	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920615.1	s__Streptomyces sp002920615	89.8791	2048	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_000716535.1	s__Streptomyces flaveolus_A	89.8361	2134	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	89.7913	2081	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	89.7385	2139	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	89.6927	2095	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCA_014649295.1	s__Streptomyces libani_A	89.2208	2005	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860525.1	s__Streptomyces rubradiris	89.1285	1932	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_900105245.1	s__Streptomyces sp900105245	88.2038	2108	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.80	95.98	0.93	0.89	5	-
GCF_014650035.1	s__Streptomyces lucensis	88.1478	1902	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649495.1	s__Streptomyces filipinensis	88.0986	2069	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_001280015.1	s__Streptomyces sp001280015	87.9191	1952	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	87.6183	2046	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_003634225.1	s__Streptomyces sp003634225	87.2393	2065	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.82	0.97	0.97	3	-
GCF_007176755.1	s__Streptomyces sp007176755	87.035	1870	3023	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	84.4446	1751	3023	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	84.2848	1716	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495685.1	s__Streptomyces sp014495685	84.2156	1586	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725125.1	s__Streptomyces toyocaensis	84.1298	1545	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	80.6401	1159	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719865.1	s__Streptomyces albus_E	80.3463	1144	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103985.1	s__Streptomyces guanduensis	79.684	1172	3023	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 14:24:24,486] [INFO] GTDB search result was written to GCF_020400685.1_ASM2040068v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:24,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:24,492] [INFO] DFAST_QC result json was written to GCF_020400685.1_ASM2040068v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:24,492] [INFO] DFAST_QC completed!
[2024-01-24 14:24:24,492] [INFO] Total running time: 0h4m40s