[2024-01-24 15:26:51,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:51,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:51,450] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference
[2024-01-24 15:26:52,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:52,909] [INFO] Task started: Prodigal
[2024-01-24 15:26:52,909] [INFO] Running command: gunzip -c /var/lib/cwl/stga2165027-b8d2-41e4-b471-b209b0d3fc83/GCF_014203595.1_ASM1420359v1_genomic.fna.gz | prodigal -d GCF_014203595.1_ASM1420359v1_genomic.fna/cds.fna -a GCF_014203595.1_ASM1420359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:21,208] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:21,209] [INFO] Task started: HMMsearch
[2024-01-24 15:27:21,209] [INFO] Running command: hmmsearch --tblout GCF_014203595.1_ASM1420359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference/reference_markers.hmm GCF_014203595.1_ASM1420359v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:21,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:21,682] [INFO] Found 6/6 markers.
[2024-01-24 15:27:21,754] [INFO] Query marker FASTA was written to GCF_014203595.1_ASM1420359v1_genomic.fna/markers.fasta
[2024-01-24 15:27:21,754] [INFO] Task started: Blastn
[2024-01-24 15:27:21,754] [INFO] Running command: blastn -query GCF_014203595.1_ASM1420359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference/reference_markers.fasta -out GCF_014203595.1_ASM1420359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:23,214] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:23,217] [INFO] Selected 25 target genomes.
[2024-01-24 15:27:23,218] [INFO] Target genome list was writen to GCF_014203595.1_ASM1420359v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:23,226] [INFO] Task started: fastANI
[2024-01-24 15:27:23,226] [INFO] Running command: fastANI --query /var/lib/cwl/stga2165027-b8d2-41e4-b471-b209b0d3fc83/GCF_014203595.1_ASM1420359v1_genomic.fna.gz --refList GCF_014203595.1_ASM1420359v1_genomic.fna/target_genomes.txt --output GCF_014203595.1_ASM1420359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:17,113] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:17,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:17,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:17,133] [INFO] Found 25 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:17,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:17,134] [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=CECT 3313	GCA_014203595.1	67293	67293	type	True	100.0	3096	3099	95	conclusive
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	99.9892	3006	3099	95	conclusive
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	92.7387	2462	3099	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	89.8235	2124	3099	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	89.8054	2096	3099	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	89.7848	2121	3099	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	89.5367	2074	3099	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	89.2292	1993	3099	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.0907	1951	3099	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	89.0847	1975	3099	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.099	2011	3099	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	88.0849	2106	3099	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	87.6139	2032	3099	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	87.4873	1987	3099	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.0732	1620	3099	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.7534	1773	3099	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	84.7255	1743	3099	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.4674	1460	3099	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.6502	1177	3099	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	80.2219	879	3099	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.7147	1212	3099	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	79.5911	1275	3099	95	below_threshold
Streptomyces bathyalis	strain=ASO4wet	GCA_015910445.1	2710756	2710756	type	True	79.2776	1041	3099	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.1642	999	3099	95	below_threshold
Tsukamurella spumae	strain=DSM 44113	GCA_012396015.1	44753	44753	type	True	75.9389	385	3099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:17,136] [INFO] DFAST Taxonomy check result was written to GCF_014203595.1_ASM1420359v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:17,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:17,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:17,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference/checkm_data
[2024-01-24 15:28:17,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:17,220] [INFO] Task started: CheckM
[2024-01-24 15:28:17,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203595.1_ASM1420359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203595.1_ASM1420359v1_genomic.fna/checkm_input GCF_014203595.1_ASM1420359v1_genomic.fna/checkm_result
[2024-01-24 15:30:30,655] [INFO] Task succeeded: CheckM
[2024-01-24 15:30:30,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:30:30,679] [INFO] ===== Completeness check finished =====
[2024-01-24 15:30:30,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:30:30,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203595.1_ASM1420359v1_genomic.fna/markers.fasta)
[2024-01-24 15:30:30,680] [INFO] Task started: Blastn
[2024-01-24 15:30:30,680] [INFO] Running command: blastn -query GCF_014203595.1_ASM1420359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ff5dc34-4cf4-4842-818a-26a4cd0b0db7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203595.1_ASM1420359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:30:32,761] [INFO] Task succeeded: Blastn
[2024-01-24 15:30:32,764] [INFO] Selected 25 target genomes.
[2024-01-24 15:30:32,764] [INFO] Target genome list was writen to GCF_014203595.1_ASM1420359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:30:32,779] [INFO] Task started: fastANI
[2024-01-24 15:30:32,779] [INFO] Running command: fastANI --query /var/lib/cwl/stga2165027-b8d2-41e4-b471-b209b0d3fc83/GCF_014203595.1_ASM1420359v1_genomic.fna.gz --refList GCF_014203595.1_ASM1420359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203595.1_ASM1420359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:31:27,063] [INFO] Task succeeded: fastANI
[2024-01-24 15:31:27,082] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:31:27,082] [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	100.0	3096	3099	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	92.7231	2464	3099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	89.9593	2118	3099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	89.9077	2158	3099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_002920615.1	s__Streptomyces sp002920615	89.8723	2092	3099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_002155905.1	s__Streptomyces tricolor	89.8522	1718	3099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	89.8254	2093	3099	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	89.6911	2161	3099	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	89.6236	2158	3099	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	89.4452	2022	3099	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	89.0994	1973	3099	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	88.2453	2156	3099	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	88.1341	1957	3099	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	88.0812	2107	3099	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	87.8767	1999	3099	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	87.6771	2078	3099	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	87.2031	2129	3099	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	87.0196	1919	3099	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	84.4323	1791	3099	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	84.3244	1616	3099	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	84.295	1768	3099	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	84.1923	1564	3099	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	80.6731	1173	3099	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	80.3535	1171	3099	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	79.6785	1221	3099	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 15:31:27,084] [INFO] GTDB search result was written to GCF_014203595.1_ASM1420359v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:31:27,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:31:27,089] [INFO] DFAST_QC result json was written to GCF_014203595.1_ASM1420359v1_genomic.fna/dqc_result.json
[2024-01-24 15:31:27,089] [INFO] DFAST_QC completed!
[2024-01-24 15:31:27,089] [INFO] Total running time: 0h4m36s