[2023-06-28 18:14:51,714] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:14:51,716] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:14:51,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference
[2023-06-28 18:14:53,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:14:53,198] [INFO] Task started: Prodigal
[2023-06-28 18:14:53,199] [INFO] Running command: gunzip -c /var/lib/cwl/stga9b61c97-545d-471a-a96d-f40b2acbbc20/GCA_020201515.1_ASM2020151v1_genomic.fna.gz | prodigal -d GCA_020201515.1_ASM2020151v1_genomic.fna/cds.fna -a GCA_020201515.1_ASM2020151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:14:58,893] [INFO] Task succeeded: Prodigal
[2023-06-28 18:14:58,894] [INFO] Task started: HMMsearch
[2023-06-28 18:14:58,894] [INFO] Running command: hmmsearch --tblout GCA_020201515.1_ASM2020151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference/reference_markers.hmm GCA_020201515.1_ASM2020151v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:14:59,158] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:14:59,160] [INFO] Found 6/6 markers.
[2023-06-28 18:14:59,186] [INFO] Query marker FASTA was written to GCA_020201515.1_ASM2020151v1_genomic.fna/markers.fasta
[2023-06-28 18:14:59,187] [INFO] Task started: Blastn
[2023-06-28 18:14:59,187] [INFO] Running command: blastn -query GCA_020201515.1_ASM2020151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference/reference_markers.fasta -out GCA_020201515.1_ASM2020151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:15:00,188] [INFO] Task succeeded: Blastn
[2023-06-28 18:15:00,193] [INFO] Selected 32 target genomes.
[2023-06-28 18:15:00,194] [INFO] Target genome list was writen to GCA_020201515.1_ASM2020151v1_genomic.fna/target_genomes.txt
[2023-06-28 18:15:00,232] [INFO] Task started: fastANI
[2023-06-28 18:15:00,233] [INFO] Running command: fastANI --query /var/lib/cwl/stga9b61c97-545d-471a-a96d-f40b2acbbc20/GCA_020201515.1_ASM2020151v1_genomic.fna.gz --refList GCA_020201515.1_ASM2020151v1_genomic.fna/target_genomes.txt --output GCA_020201515.1_ASM2020151v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:15:40,030] [INFO] Task succeeded: fastANI
[2023-06-28 18:15:40,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:15:40,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:15:40,054] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:15:40,054] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:15:40,054] [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
Carbonactinospora thermoautotrophica	strain=UBT1	GCA_001543915.1	1469144	1469144	type	True	76.6284	105	608	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	76.5979	161	608	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	76.5083	161	608	95	below_threshold
Carbonactinospora thermoautotrophica	strain=UBT1	GCA_001543895.1	1469144	1469144	type	True	76.4705	142	608	95	below_threshold
Frankia coriariae	strain=BMG5.1	GCA_001017755.1	1562887	1562887	type	True	76.4701	121	608	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.3437	161	608	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	76.2789	128	608	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	76.2587	172	608	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	76.2506	160	608	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	76.1878	93	608	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	76.1633	199	608	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	76.1597	150	608	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	76.1562	153	608	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	76.1508	142	608	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	76.1473	138	608	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	76.1334	122	608	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	76.1057	114	608	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	76.0844	167	608	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	76.0772	137	608	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	76.0683	159	608	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	76.0543	145	608	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.0418	160	608	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.0324	163	608	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	76.0195	168	608	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	76.0042	165	608	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	75.9928	132	608	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	75.9766	166	608	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	75.9242	145	608	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	75.8968	173	608	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	75.847	140	608	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	75.6974	173	608	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	75.5308	154	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:15:40,057] [INFO] DFAST Taxonomy check result was written to GCA_020201515.1_ASM2020151v1_genomic.fna/tc_result.tsv
[2023-06-28 18:15:40,058] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:15:40,058] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:15:40,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference/checkm_data
[2023-06-28 18:15:40,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:15:40,096] [INFO] Task started: CheckM
[2023-06-28 18:15:40,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020201515.1_ASM2020151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020201515.1_ASM2020151v1_genomic.fna/checkm_input GCA_020201515.1_ASM2020151v1_genomic.fna/checkm_result
[2023-06-28 18:16:03,268] [INFO] Task succeeded: CheckM
[2023-06-28 18:16:03,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:16:03,298] [INFO] ===== Completeness check finished =====
[2023-06-28 18:16:03,298] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:16:03,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020201515.1_ASM2020151v1_genomic.fna/markers.fasta)
[2023-06-28 18:16:03,299] [INFO] Task started: Blastn
[2023-06-28 18:16:03,299] [INFO] Running command: blastn -query GCA_020201515.1_ASM2020151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb482a8b7-7a54-4da7-a3ef-db19c131da03/dqc_reference/reference_markers_gtdb.fasta -out GCA_020201515.1_ASM2020151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:16:04,730] [INFO] Task succeeded: Blastn
[2023-06-28 18:16:04,739] [INFO] Selected 32 target genomes.
[2023-06-28 18:16:04,739] [INFO] Target genome list was writen to GCA_020201515.1_ASM2020151v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:16:04,802] [INFO] Task started: fastANI
[2023-06-28 18:16:04,802] [INFO] Running command: fastANI --query /var/lib/cwl/stga9b61c97-545d-471a-a96d-f40b2acbbc20/GCA_020201515.1_ASM2020151v1_genomic.fna.gz --refList GCA_020201515.1_ASM2020151v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020201515.1_ASM2020151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:16:31,253] [INFO] Task succeeded: fastANI
[2023-06-28 18:16:31,283] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:16:31,284] [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
GCA_017882835.1	s__JADGOU01 sp017882835	77.3448	116	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__JADGOU01;g__JADGOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650445.1	s__JAENVS01 sp016650445	76.9802	178	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__SCTD01;g__JAENVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805775.1	s__SCTD01 sp902805775	76.9731	158	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__SCTD01;g__SCTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882765.1	s__JADGOW01 sp017882765	76.8139	83	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__JADGOW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594885.1	s__Vallicoccus soli	76.7345	187	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Vallicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216915.1	s__Motilibacter rhizosphaerae	76.6089	160	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634695.1	s__Motilibacter peucedani	76.5181	160	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805805.1	s__SCTD01 sp902805805	76.5162	143	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__SCTD01;g__SCTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543895.1	s__Carbonactinospora thermoautotrophica	76.4728	142	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Carbonactinosporaceae;g__Carbonactinospora	95.0	99.44	99.44	0.88	0.88	2	-
GCA_004297305.1	s__FW305-bin1 sp004297305	76.4018	81	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__FW305-bin1;g__FW305-bin1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250645.1	s__Motilibacter_A aurantiacus	76.3657	159	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	76.2301	137	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725415.1	s__Pseudonocardia sp001725415	76.2174	163	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCF_007483665.1	s__Catellatospora sichuanensis	76.1772	151	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	76.1604	137	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	76.1588	150	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272695.1	s__Nocardioides sp012272695	76.143	86	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720385.1	s__Catellatospora vulcania	76.0837	167	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	76.076	165	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	76.0752	145	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_014648555.1	s__Kitasatospora griseola	76.0642	144	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.80	97.68	0.89	0.89	3	-
GCF_001854805.1	s__Frankia sp001854805	76.0639	187	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	76.0485	161	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583555.1	s__Pseudonocardia sp002583555	76.0481	147	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006912135.1	s__Cryptosporangium phraense	76.0426	162	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845675.1	s__Lentzea sp007845675	76.0332	161	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595675.1	s__Saccharomonospora sp016595675	76.0048	131	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648355.1	s__Actinoplanes azureus	75.9944	163	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552175.1	s__Spirillospora kijaniata	75.9941	166	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_001905465.1	s__Kitasatospora sp001905465	75.9794	152	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	75.8547	139	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006715865.1	s__Cellulomonas sp006715865	75.6124	146	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:16:31,286] [INFO] GTDB search result was written to GCA_020201515.1_ASM2020151v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:16:31,286] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:16:31,293] [INFO] DFAST_QC result json was written to GCA_020201515.1_ASM2020151v1_genomic.fna/dqc_result.json
[2023-06-28 18:16:31,293] [INFO] DFAST_QC completed!
[2023-06-28 18:16:31,293] [INFO] Total running time: 0h1m40s