[2024-01-24 13:48:42,778] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:42,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:42,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference
[2024-01-24 13:48:44,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,022] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fbbacd5-34dd-44e8-bd27-16bd5d33923e/GCF_004362825.1_ASM436282v1_genomic.fna.gz | prodigal -d GCF_004362825.1_ASM436282v1_genomic.fna/cds.fna -a GCF_004362825.1_ASM436282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:11,389] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:11,389] [INFO] Task started: HMMsearch
[2024-01-24 13:49:11,389] [INFO] Running command: hmmsearch --tblout GCF_004362825.1_ASM436282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference/reference_markers.hmm GCF_004362825.1_ASM436282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:11,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:11,768] [INFO] Found 6/6 markers.
[2024-01-24 13:49:11,833] [INFO] Query marker FASTA was written to GCF_004362825.1_ASM436282v1_genomic.fna/markers.fasta
[2024-01-24 13:49:11,833] [INFO] Task started: Blastn
[2024-01-24 13:49:11,833] [INFO] Running command: blastn -query GCF_004362825.1_ASM436282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference/reference_markers.fasta -out GCF_004362825.1_ASM436282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:13,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:13,148] [INFO] Selected 28 target genomes.
[2024-01-24 13:49:13,148] [INFO] Target genome list was writen to GCF_004362825.1_ASM436282v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:13,157] [INFO] Task started: fastANI
[2024-01-24 13:49:13,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fbbacd5-34dd-44e8-bd27-16bd5d33923e/GCF_004362825.1_ASM436282v1_genomic.fna.gz --refList GCF_004362825.1_ASM436282v1_genomic.fna/target_genomes.txt --output GCF_004362825.1_ASM436282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:01,129] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:01,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:01,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:01,152] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:01,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:01,153] [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
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	79.3382	938	2763	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	79.326	923	2763	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	79.3249	945	2763	95	below_threshold
Actinokineospora xionganensis	strain=HBU206404	GCA_014323725.1	2684470	2684470	type	True	79.2689	916	2763	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	79.2488	893	2763	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	79.22	1022	2763	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	79.2106	942	2763	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	79.176	946	2763	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	79.1346	965	2763	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	78.9804	1042	2763	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	78.9381	983	2763	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	78.6879	973	2763	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	78.6107	1064	2763	95	below_threshold
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	78.6024	964	2763	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.5889	980	2763	95	below_threshold
Amycolatopsis suaedae	strain=8-3EHSu	GCA_004214935.1	2510978	2510978	type	True	78.5581	952	2763	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	78.54	1119	2763	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	78.4875	916	2763	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	78.4326	1101	2763	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	78.4076	1034	2763	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	78.3122	978	2763	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	78.3043	984	2763	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	78.2803	947	2763	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.26	857	2763	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.2435	943	2763	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	78.2197	864	2763	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	78.1603	800	2763	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	76.3982	544	2763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,155] [INFO] DFAST Taxonomy check result was written to GCF_004362825.1_ASM436282v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:01,156] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:01,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:01,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference/checkm_data
[2024-01-24 13:50:01,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:01,237] [INFO] Task started: CheckM
[2024-01-24 13:50:01,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362825.1_ASM436282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362825.1_ASM436282v1_genomic.fna/checkm_input GCF_004362825.1_ASM436282v1_genomic.fna/checkm_result
[2024-01-24 13:52:01,104] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:01,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:01,131] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:01,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:01,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362825.1_ASM436282v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:01,132] [INFO] Task started: Blastn
[2024-01-24 13:52:01,132] [INFO] Running command: blastn -query GCF_004362825.1_ASM436282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ce8596f-ee5b-4279-9f01-40758e5cb8c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362825.1_ASM436282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:03,130] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:03,133] [INFO] Selected 25 target genomes.
[2024-01-24 13:52:03,133] [INFO] Target genome list was writen to GCF_004362825.1_ASM436282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:03,177] [INFO] Task started: fastANI
[2024-01-24 13:52:03,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fbbacd5-34dd-44e8-bd27-16bd5d33923e/GCF_004362825.1_ASM436282v1_genomic.fna.gz --refList GCF_004362825.1_ASM436282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362825.1_ASM436282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:48,843] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:48,876] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:48,876] [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_004362825.1	s__Labedaea rhizosphaerae	100.0	2761	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907695.1	s__Actinokineospora baliensis	79.336	921	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	79.3225	939	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_014323725.1	s__Actinokineospora xionganensis	79.2846	913	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	79.272	891	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	79.1693	1049	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_009745975.1	s__Actinokineospora pegani	79.1545	952	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	79.0306	995	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	78.9628	1048	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	78.9499	981	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	78.6866	972	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013280595.1	s__Kibdelosporangium persicum	78.5697	970	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387475.1	s__Kutzneria buriramensis	78.476	1104	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	78.4744	919	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	78.4242	1041	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875555.1	s__Amycolatopsis magusensis	78.4082	1033	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002815.1	s__Umezawaea tangerina	78.3607	1094	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	78.3347	971	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205015.1	s__Actinosynnema ecbatanense	78.3174	981	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176515.1	s__Kibdelosporangium aridum	78.3028	928	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	78.2667	1033	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100275.1	s__Lentzea violacea	78.2153	866	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	78.1472	808	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552155.1	s__Spirillospora formosensis	76.4022	544	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013364275.1	s__Spirillospora sp013364275	76.2267	789	2763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:48,878] [INFO] GTDB search result was written to GCF_004362825.1_ASM436282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:48,878] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:48,884] [INFO] DFAST_QC result json was written to GCF_004362825.1_ASM436282v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:48,884] [INFO] DFAST_QC completed!
[2024-01-24 13:52:48,885] [INFO] Total running time: 0h4m6s