[2024-01-24 13:24:12,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,449] [INFO] DQC Reference Directory: /var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference
[2024-01-24 13:24:13,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,685] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,685] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeb08264-9bca-436a-b283-c3dbda8ba0db/GCF_014646055.1_ASM1464605v1_genomic.fna.gz | prodigal -d GCF_014646055.1_ASM1464605v1_genomic.fna/cds.fna -a GCF_014646055.1_ASM1464605v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:40,210] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:40,210] [INFO] Task started: HMMsearch
[2024-01-24 13:24:40,210] [INFO] Running command: hmmsearch --tblout GCF_014646055.1_ASM1464605v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference/reference_markers.hmm GCF_014646055.1_ASM1464605v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:40,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:40,515] [INFO] Found 6/6 markers.
[2024-01-24 13:24:40,574] [INFO] Query marker FASTA was written to GCF_014646055.1_ASM1464605v1_genomic.fna/markers.fasta
[2024-01-24 13:24:40,574] [INFO] Task started: Blastn
[2024-01-24 13:24:40,574] [INFO] Running command: blastn -query GCF_014646055.1_ASM1464605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference/reference_markers.fasta -out GCF_014646055.1_ASM1464605v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:41,904] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:41,907] [INFO] Selected 37 target genomes.
[2024-01-24 13:24:41,907] [INFO] Target genome list was writen to GCF_014646055.1_ASM1464605v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:41,953] [INFO] Task started: fastANI
[2024-01-24 13:24:41,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb08264-9bca-436a-b283-c3dbda8ba0db/GCF_014646055.1_ASM1464605v1_genomic.fna.gz --refList GCF_014646055.1_ASM1464605v1_genomic.fna/target_genomes.txt --output GCF_014646055.1_ASM1464605v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:37,583] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:37,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:37,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:37,609] [INFO] Found 37 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:25:37,609] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:25:37,609] [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
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	80.5303	1000	2748	95	below_threshold
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	80.4353	1014	2748	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.4279	1025	2748	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	80.3695	947	2748	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	80.1303	1007	2748	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	80.0598	899	2748	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	79.9544	1035	2748	95	below_threshold
Streptomyces sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	79.9348	1060	2748	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	79.8651	1095	2748	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.8441	1048	2748	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	79.8109	812	2748	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	79.7826	1037	2748	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	79.7803	1025	2748	95	below_threshold
Streptomyces violens	strain=NRRL ISP-5597	GCA_000717745.1	66377	66377	type	True	79.7769	1009	2748	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.7397	876	2748	95	below_threshold
Streptomyces purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	79.7202	933	2748	95	below_threshold
Streptomyces ochraceiscleroticus	strain=NRRL ISP-5594	GCA_000720485.1	47761	47761	type	True	79.7072	1031	2748	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	79.7049	1075	2748	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	79.6796	1048	2748	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	79.6773	1039	2748	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	79.6679	1112	2748	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	79.6655	999	2748	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	79.6511	1097	2748	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.6478	1010	2748	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	79.6361	1063	2748	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	79.6312	1121	2748	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	79.6039	1109	2748	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	79.5965	1080	2748	95	below_threshold
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	79.5838	1133	2748	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	79.578	1004	2748	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	79.4816	1049	2748	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.297	1151	2748	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	78.9972	915	2748	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	78.9385	1041	2748	95	below_threshold
Streptomyces armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	78.7996	1042	2748	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	78.6474	986	2748	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	78.6048	1011	2748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:37,611] [INFO] DFAST Taxonomy check result was written to GCF_014646055.1_ASM1464605v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:37,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:37,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:37,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference/checkm_data
[2024-01-24 13:25:37,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:37,688] [INFO] Task started: CheckM
[2024-01-24 13:25:37,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646055.1_ASM1464605v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646055.1_ASM1464605v1_genomic.fna/checkm_input GCF_014646055.1_ASM1464605v1_genomic.fna/checkm_result
[2024-01-24 13:27:15,855] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:15,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:15,877] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:15,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:15,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646055.1_ASM1464605v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:15,878] [INFO] Task started: Blastn
[2024-01-24 13:27:15,878] [INFO] Running command: blastn -query GCF_014646055.1_ASM1464605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb189d680-c7c4-431a-84e5-e5586a3c9edd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646055.1_ASM1464605v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:17,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:17,980] [INFO] Selected 30 target genomes.
[2024-01-24 13:27:17,980] [INFO] Target genome list was writen to GCF_014646055.1_ASM1464605v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:18,116] [INFO] Task started: fastANI
[2024-01-24 13:27:18,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb08264-9bca-436a-b283-c3dbda8ba0db/GCF_014646055.1_ASM1464605v1_genomic.fna.gz --refList GCF_014646055.1_ASM1464605v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646055.1_ASM1464605v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:05,719] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:05,742] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:05,742] [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_014646055.1	s__Streptomyces_A tyrosinilyticus	100.0	2743	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003144095.1	s__Streptomyces sp003144095	80.7231	980	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	80.6355	1019	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380165.1	s__Streptomyces_A vitaminophilus	80.539	999	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	99.94	99.94	0.99	0.99	2	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	80.3109	957	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	80.0038	1085	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014648775.1	s__Streptomyces abikoensis	79.9879	1030	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCA_003519485.1	s__Streptomyces sp003519485	79.9519	637	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	79.8992	1124	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999195.1	s__Streptomyces sp003999195	79.8898	1033	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417735.1	s__Streptomyces sp001417735	79.815	1113	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805335.1	s__Streptomyces sp000805335	79.8142	1012	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	79.8113	1035	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	79.8096	1108	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
GCF_002813405.1	s__Streptomyces sp002813405	79.8028	1086	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122735.1	s__Streptomyces sioyaensis	79.7817	1025	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_000717745.1	s__Streptomyces violens	79.7746	1011	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0121	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	79.7474	1107	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373585.1	s__Streptomyces sp000373585	79.7358	1079	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905385.1	s__Streptomyces sp001905385	79.7161	1072	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_000720485.1	s__Streptomyces ochraceiscleroticus	79.7077	1032	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0121	N/A	N/A	N/A	N/A	1	-
GCF_009811555.1	s__Streptomyces caniferus	79.6776	1112	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	79.6702	999	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_014648695.1	s__Streptomyces albospinus	79.6354	1048	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811595.1	s__Streptomyces libani	79.584	1133	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009834125.1	s__Streptomyces sp009834125	79.5825	1092	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	79.5172	1103	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	79.4975	1004	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639205.1	s__Streptomyces nojiriensis	79.4124	1101	2748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000482585.1	s__Streptomyces sp000482585	78.8787	923	2748	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 13:28:05,744] [INFO] GTDB search result was written to GCF_014646055.1_ASM1464605v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:05,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:05,750] [INFO] DFAST_QC result json was written to GCF_014646055.1_ASM1464605v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:05,750] [INFO] DFAST_QC completed!
[2024-01-24 13:28:05,750] [INFO] Total running time: 0h3m53s