[2024-01-24 14:06:03,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:03,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:03,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference
[2024-01-24 14:06:04,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:04,765] [INFO] Task started: Prodigal
[2024-01-24 14:06:04,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg46d8c33e-32e7-4102-b6bd-640ba59cbea9/GCF_014646155.1_ASM1464615v1_genomic.fna.gz | prodigal -d GCF_014646155.1_ASM1464615v1_genomic.fna/cds.fna -a GCF_014646155.1_ASM1464615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:32,152] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:32,152] [INFO] Task started: HMMsearch
[2024-01-24 14:06:32,152] [INFO] Running command: hmmsearch --tblout GCF_014646155.1_ASM1464615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference/reference_markers.hmm GCF_014646155.1_ASM1464615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:32,623] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:32,625] [INFO] Found 6/6 markers.
[2024-01-24 14:06:32,683] [INFO] Query marker FASTA was written to GCF_014646155.1_ASM1464615v1_genomic.fna/markers.fasta
[2024-01-24 14:06:32,684] [INFO] Task started: Blastn
[2024-01-24 14:06:32,684] [INFO] Running command: blastn -query GCF_014646155.1_ASM1464615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference/reference_markers.fasta -out GCF_014646155.1_ASM1464615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:33,857] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:33,860] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:33,861] [INFO] Target genome list was writen to GCF_014646155.1_ASM1464615v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:33,878] [INFO] Task started: fastANI
[2024-01-24 14:06:33,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d8c33e-32e7-4102-b6bd-640ba59cbea9/GCF_014646155.1_ASM1464615v1_genomic.fna.gz --refList GCF_014646155.1_ASM1464615v1_genomic.fna/target_genomes.txt --output GCF_014646155.1_ASM1464615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:18,771] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:18,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:18,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:18,788] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:18,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:18,789] [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
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	80.5	1316	2444	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	80.4436	1236	2444	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	80.4013	1276	2444	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	80.3379	1283	2444	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	80.2241	1027	2444	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	80.1876	1152	2444	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	80.1582	1102	2444	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	80.1143	1161	2444	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	80.0789	1137	2444	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	79.8772	1245	2444	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	79.8555	1242	2444	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	79.8411	1237	2444	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	79.7735	1278	2444	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	79.737	1153	2444	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	79.7211	1190	2444	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	79.6446	1208	2444	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	79.6024	1234	2444	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	79.5662	1111	2444	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.4901	1139	2444	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.8965	715	2444	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.6311	926	2444	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	77.9048	1018	2444	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.0751	913	2444	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.141	568	2444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:18,791] [INFO] DFAST Taxonomy check result was written to GCF_014646155.1_ASM1464615v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:18,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:18,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:18,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference/checkm_data
[2024-01-24 14:07:18,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:18,860] [INFO] Task started: CheckM
[2024-01-24 14:07:18,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646155.1_ASM1464615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646155.1_ASM1464615v1_genomic.fna/checkm_input GCF_014646155.1_ASM1464615v1_genomic.fna/checkm_result
[2024-01-24 14:08:55,227] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:55,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:55,256] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:55,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:55,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646155.1_ASM1464615v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:55,257] [INFO] Task started: Blastn
[2024-01-24 14:08:55,257] [INFO] Running command: blastn -query GCF_014646155.1_ASM1464615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d9c869-4ca4-4838-8c1b-4cb84d527230/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646155.1_ASM1464615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:56,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:56,919] [INFO] Selected 19 target genomes.
[2024-01-24 14:08:56,919] [INFO] Target genome list was writen to GCF_014646155.1_ASM1464615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:56,936] [INFO] Task started: fastANI
[2024-01-24 14:08:56,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d8c33e-32e7-4102-b6bd-640ba59cbea9/GCF_014646155.1_ASM1464615v1_genomic.fna.gz --refList GCF_014646155.1_ASM1464615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646155.1_ASM1464615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:33,901] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:33,924] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:33,924] [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_014646155.1	s__Actinoplanes endophyticus	100.0	2441	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862275.1	s__Actinoplanes nipponensis	80.5173	1311	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648355.1	s__Actinoplanes azureus	80.4366	1108	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	80.3416	1282	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	80.2556	1263	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	80.2333	1229	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	80.2011	1148	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_003751945.1	s__Actinoplanes caeruleus	80.1882	1096	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	80.1481	1091	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	80.0896	1236	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	79.9376	1232	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	79.9088	1231	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	79.8763	1109	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	79.7771	1143	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014205225.1	s__Actinoplanes octamycinicus	79.7154	1291	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016785085.1	s__Actinoplanes sp016785085	79.6702	1202	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	79.5996	1222	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_017592555.1	s__Actinoplanes sp017592555	79.4914	1142	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	79.1707	1077	2444	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:33,926] [INFO] GTDB search result was written to GCF_014646155.1_ASM1464615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:33,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:33,931] [INFO] DFAST_QC result json was written to GCF_014646155.1_ASM1464615v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:33,932] [INFO] DFAST_QC completed!
[2024-01-24 14:09:33,932] [INFO] Total running time: 0h3m30s