[2024-01-24 13:36:45,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference
[2024-01-24 13:36:47,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,108] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,109] [INFO] Running command: gunzip -c /var/lib/cwl/stgec7aa443-5fd7-4f55-bfab-88ad3ba7ca74/GCF_014650035.1_ASM1465003v1_genomic.fna.gz | prodigal -d GCF_014650035.1_ASM1465003v1_genomic.fna/cds.fna -a GCF_014650035.1_ASM1465003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:09,869] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:09,869] [INFO] Task started: HMMsearch
[2024-01-24 13:37:09,869] [INFO] Running command: hmmsearch --tblout GCF_014650035.1_ASM1465003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference/reference_markers.hmm GCF_014650035.1_ASM1465003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:10,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:10,235] [INFO] Found 6/6 markers.
[2024-01-24 13:37:10,304] [INFO] Query marker FASTA was written to GCF_014650035.1_ASM1465003v1_genomic.fna/markers.fasta
[2024-01-24 13:37:10,304] [INFO] Task started: Blastn
[2024-01-24 13:37:10,304] [INFO] Running command: blastn -query GCF_014650035.1_ASM1465003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference/reference_markers.fasta -out GCF_014650035.1_ASM1465003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:11,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:11,713] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:11,714] [INFO] Target genome list was writen to GCF_014650035.1_ASM1465003v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:11,745] [INFO] Task started: fastANI
[2024-01-24 13:37:11,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgec7aa443-5fd7-4f55-bfab-88ad3ba7ca74/GCF_014650035.1_ASM1465003v1_genomic.fna.gz --refList GCF_014650035.1_ASM1465003v1_genomic.fna/target_genomes.txt --output GCF_014650035.1_ASM1465003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:58,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:58,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:58,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:58,857] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:58,857] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:58,857] [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 olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	88.3578	1860	2551	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	88.3278	1857	2551	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	88.3098	1842	2551	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	88.2685	1903	2551	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	88.2173	1881	2551	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	88.2165	1862	2551	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	88.1807	1948	2551	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.135	1825	2551	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	88.0965	1868	2551	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	88.089	1867	2551	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	87.8507	1844	2551	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	87.6445	1746	2551	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	87.6229	1797	2551	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	87.4512	1728	2551	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	87.372	1771	2551	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	87.3163	1845	2551	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	87.2781	1877	2551	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.1103	1622	2551	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.9475	1611	2551	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.6947	1371	2551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,859] [INFO] DFAST Taxonomy check result was written to GCF_014650035.1_ASM1465003v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:58,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:58,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:58,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference/checkm_data
[2024-01-24 13:37:58,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:58,935] [INFO] Task started: CheckM
[2024-01-24 13:37:58,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650035.1_ASM1465003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650035.1_ASM1465003v1_genomic.fna/checkm_input GCF_014650035.1_ASM1465003v1_genomic.fna/checkm_result
[2024-01-24 13:39:46,033] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:46,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:46,055] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:46,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:46,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650035.1_ASM1465003v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:46,056] [INFO] Task started: Blastn
[2024-01-24 13:39:46,056] [INFO] Running command: blastn -query GCF_014650035.1_ASM1465003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46075507-c737-4fc1-a1d1-e75ae09c29b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650035.1_ASM1465003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:48,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:48,142] [INFO] Selected 20 target genomes.
[2024-01-24 13:39:48,142] [INFO] Target genome list was writen to GCF_014650035.1_ASM1465003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:48,175] [INFO] Task started: fastANI
[2024-01-24 13:39:48,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgec7aa443-5fd7-4f55-bfab-88ad3ba7ca74/GCF_014650035.1_ASM1465003v1_genomic.fna.gz --refList GCF_014650035.1_ASM1465003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650035.1_ASM1465003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:32,885] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:32,901] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:32,901] [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_014650035.1	s__Streptomyces lucensis	100.0	2547	2551	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_000716535.1	s__Streptomyces flaveolus_A	88.4411	1854	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_013046785.1	s__Streptomyces sp013046785	88.4408	1818	2551	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	88.4283	1826	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_017526105.1	s__Streptomyces cyanogenus	88.3953	1902	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	88.365	1858	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_014203595.1	s__Streptomyces echinatus	88.243	1907	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741855.1	s__Streptomyces musisoli	88.189	1947	2551	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	88.0936	1867	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_002155905.1	s__Streptomyces tricolor	88.0483	1532	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_016741775.1	s__Streptomyces actinomycinicus	88.015	1886	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	87.8763	1840	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	87.8109	1737	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718775.1	s__Streptomyces sp000718775	87.8039	1723	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	87.7828	1817	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000444875.1	s__Streptomyces collinus_A	87.7072	1817	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.10	97.10	0.84	0.84	2	-
GCA_016432725.1	s__Streptomyces sp016432725	87.7067	1859	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953885.1	s__Streptomyces sp001953885	87.6339	1787	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542625.1	s__Streptomyces griseochromogenes	87.3421	1867	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014651035.1	s__Streptomyces lomondensis	84.8663	1610	2551	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 13:40:32,903] [INFO] GTDB search result was written to GCF_014650035.1_ASM1465003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:32,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:32,908] [INFO] DFAST_QC result json was written to GCF_014650035.1_ASM1465003v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:32,908] [INFO] DFAST_QC completed!
[2024-01-24 13:40:32,908] [INFO] Total running time: 0h3m47s