[2024-01-24 13:17:30,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:30,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:30,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference
[2024-01-24 13:17:31,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:31,405] [INFO] Task started: Prodigal
[2024-01-24 13:17:31,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg3074110c-66bd-4c7a-ad87-6fe0f65d6298/GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna.gz | prodigal -d GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/cds.fna -a GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:52,285] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:52,286] [INFO] Task started: HMMsearch
[2024-01-24 13:17:52,286] [INFO] Running command: hmmsearch --tblout GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference/reference_markers.hmm GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:52,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:52,650] [INFO] Found 6/6 markers.
[2024-01-24 13:17:52,721] [INFO] Query marker FASTA was written to GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/markers.fasta
[2024-01-24 13:17:52,721] [INFO] Task started: Blastn
[2024-01-24 13:17:52,721] [INFO] Running command: blastn -query GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference/reference_markers.fasta -out GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:54,042] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:54,045] [INFO] Selected 18 target genomes.
[2024-01-24 13:17:54,046] [INFO] Target genome list was writen to GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/target_genomes.txt
[2024-01-24 13:17:54,053] [INFO] Task started: fastANI
[2024-01-24 13:17:54,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg3074110c-66bd-4c7a-ad87-6fe0f65d6298/GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna.gz --refList GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/target_genomes.txt --output GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:22,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:22,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:22,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:22,271] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:22,271] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:22,272] [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
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	100.0	2332	2337	95	inconclusive
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	96.1576	1986	2337	95	inconclusive
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	94.8681	1923	2337	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	89.2271	1763	2337	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	87.5115	1585	2337	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	87.4658	1581	2337	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	87.1726	1440	2337	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	83.4784	1342	2337	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.4332	1300	2337	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	83.4124	1314	2337	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	83.4049	1311	2337	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	82.6727	1023	2337	95	below_threshold
Nocardiopsis salina	strain=YIM 90010	GCA_000341025.1	245836	245836	type	True	81.5122	1040	2337	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.3965	984	2337	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.198	710	2337	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.1046	738	2337	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	76.9871	441	2337	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	76.545	511	2337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:22,274] [INFO] DFAST Taxonomy check result was written to GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/tc_result.tsv
[2024-01-24 13:18:22,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:22,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:22,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference/checkm_data
[2024-01-24 13:18:22,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:22,345] [INFO] Task started: CheckM
[2024-01-24 13:18:22,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/checkm_input GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/checkm_result
[2024-01-24 13:19:24,217] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:24,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:24,241] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:24,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:24,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/markers.fasta)
[2024-01-24 13:19:24,243] [INFO] Task started: Blastn
[2024-01-24 13:19:24,243] [INFO] Running command: blastn -query GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c8ba2a0-169a-44a5-ae56-702058903dfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,174] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,183] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:26,184] [INFO] Target genome list was writen to GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:26,192] [INFO] Task started: fastANI
[2024-01-24 13:19:26,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg3074110c-66bd-4c7a-ad87-6fe0f65d6298/GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna.gz --refList GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/target_genomes_gtdb.txt --output GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:49,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:49,863] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:49,864] [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_000340985.1	s__Nocardiopsis valliformis	100.0	2332	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014201115.1	s__Nocardiopsis metallicus	94.8708	1924	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	89.2175	1765	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651695.1	s__Nocardiopsis terrae	87.5072	1585	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000341265.1	s__Nocardiopsis prasina	87.1815	1439	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCA_018388625.1	s__Nocardiopsis sp018388625	86.9114	1495	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341225.1	s__Nocardiopsis alba	84.2411	1306	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	98.86	98.56	0.95	0.95	4	-
GCA_002529455.1	s__Nocardiopsis fusca	83.6361	1336	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	83.4746	1347	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_012396365.1	s__Nocardiopsis alborubida	83.4361	1311	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_003386285.1	s__Nocardiopsis sp003386285	82.7166	1256	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	82.651	1027	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203695.1	s__Nocardiopsis algeriensis	82.5012	1068	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341025.1	s__Nocardiopsis salina	81.5013	1042	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	78.826	741	2337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,865] [INFO] GTDB search result was written to GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:49,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:49,870] [INFO] DFAST_QC result json was written to GCF_000340985.1_genetic_mechanisms_of_environmental_adaptability_genomic.fna/dqc_result.json
[2024-01-24 13:19:49,870] [INFO] DFAST_QC completed!
[2024-01-24 13:19:49,870] [INFO] Total running time: 0h2m20s