[2024-01-24 12:29:52,509] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference
[2024-01-24 12:29:53,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,691] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d27f037-4340-4b6a-8e37-3e2441f6da29/GCF_014640475.1_ASM1464047v1_genomic.fna.gz | prodigal -d GCF_014640475.1_ASM1464047v1_genomic.fna/cds.fna -a GCF_014640475.1_ASM1464047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:05,162] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:05,162] [INFO] Task started: HMMsearch
[2024-01-24 12:30:05,162] [INFO] Running command: hmmsearch --tblout GCF_014640475.1_ASM1464047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference/reference_markers.hmm GCF_014640475.1_ASM1464047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:05,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:05,467] [INFO] Found 6/6 markers.
[2024-01-24 12:30:05,528] [INFO] Query marker FASTA was written to GCF_014640475.1_ASM1464047v1_genomic.fna/markers.fasta
[2024-01-24 12:30:05,529] [INFO] Task started: Blastn
[2024-01-24 12:30:05,529] [INFO] Running command: blastn -query GCF_014640475.1_ASM1464047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference/reference_markers.fasta -out GCF_014640475.1_ASM1464047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:06,564] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:06,568] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:06,568] [INFO] Target genome list was writen to GCF_014640475.1_ASM1464047v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:06,575] [INFO] Task started: fastANI
[2024-01-24 12:30:06,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d27f037-4340-4b6a-8e37-3e2441f6da29/GCF_014640475.1_ASM1464047v1_genomic.fna.gz --refList GCF_014640475.1_ASM1464047v1_genomic.fna/target_genomes.txt --output GCF_014640475.1_ASM1464047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:24,914] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:24,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:24,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:24,928] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:24,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:24,929] [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
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	100.0	1308	1308	95	conclusive
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	99.9991	1305	1308	95	conclusive
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	78.6426	602	1308	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	77.2548	356	1308	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.9218	264	1308	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	75.6466	263	1308	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	75.5401	291	1308	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	75.4963	347	1308	95	below_threshold
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	75.4939	297	1308	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	75.4823	265	1308	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	75.4356	281	1308	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	75.3595	285	1308	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	75.3549	232	1308	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	75.3382	249	1308	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	75.3253	368	1308	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	75.3044	262	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:24,932] [INFO] DFAST Taxonomy check result was written to GCF_014640475.1_ASM1464047v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:24,933] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:24,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:24,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference/checkm_data
[2024-01-24 12:30:24,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:24,978] [INFO] Task started: CheckM
[2024-01-24 12:30:24,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640475.1_ASM1464047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640475.1_ASM1464047v1_genomic.fna/checkm_input GCF_014640475.1_ASM1464047v1_genomic.fna/checkm_result
[2024-01-24 12:31:25,965] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:25,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:25,986] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:25,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:25,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640475.1_ASM1464047v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:25,987] [INFO] Task started: Blastn
[2024-01-24 12:31:25,987] [INFO] Running command: blastn -query GCF_014640475.1_ASM1464047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aa536bf-13c1-45c4-8d2b-c317a009d84d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640475.1_ASM1464047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:27,629] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:27,633] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:27,633] [INFO] Target genome list was writen to GCF_014640475.1_ASM1464047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:27,647] [INFO] Task started: fastANI
[2024-01-24 12:31:27,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d27f037-4340-4b6a-8e37-3e2441f6da29/GCF_014640475.1_ASM1464047v1_genomic.fna.gz --refList GCF_014640475.1_ASM1464047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640475.1_ASM1464047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:40,839] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:40,857] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:40,857] [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_004300825.1	s__Egicoccus halophilus	99.9991	1305	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018335555.1	s__Egicoccus sp018335555	81.2555	517	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133465.1	s__SLMP01 sp007133465	79.1044	383	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLMP01	95.0	99.22	99.05	0.81	0.81	3	-
GCF_000969705.1	s__Nitriliruptor alkaliphilus	78.6206	606	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Nitriliruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003558435.1	s__PWLR01 sp003558435	78.4462	463	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__PWLR01	95.0	99.63	99.63	0.94	0.94	2	-
GCA_007120465.1	s__CSSed11-175R1 sp007120465	78.4328	361	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130695.1	s__SKLC01 sp007130695	78.4005	390	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKLC01	95.0	99.35	99.35	0.92	0.92	2	-
GCA_007123425.1	s__SKLC01 sp007123425	78.3756	313	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121975.1	s__SKJO01 sp007121975	78.1667	309	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118045.1	s__SKTG01 sp007118045	78.0863	365	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003554005.1	s__T1Sed10-7 sp003554005	78.0612	305	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.88	98.67	0.78	0.76	5	-
GCA_007136095.1	s__CSSed11-175R1 sp007136095	78.0245	338	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	99.27	97.70	0.87	0.80	7	-
GCA_007117945.1	s__T1Sed10-7 sp007117945	77.8107	286	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120485.1	s__SKTG01 sp007120485	77.7792	293	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	98.43	98.43	0.68	0.68	2	-
GCA_007121785.1	s__SKTG01 sp007121785	77.7701	377	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	99.65	99.65	0.87	0.87	2	-
GCA_018401275.1	s__CSBr16-57R1 sp018401275	77.7329	230	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSBr16-57R1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131525.1	s__T1Sed10-7 sp007131525	77.6717	261	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.34	98.34	0.77	0.77	2	-
GCA_007125475.1	s__SLDB01 sp007125475	77.4651	296	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLDB01	95.0	98.81	98.81	0.77	0.77	2	-
GCA_017852335.1	s__CSBr16-57R1 sp017852335	77.0467	247	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSBr16-57R1	95.0	99.66	99.60	0.93	0.91	3	-
GCA_003553565.1	s__PUKE01 sp003553565	76.1881	240	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__PUKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862515.1	s__Asanoa iriomotensis	75.3312	366	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:40,859] [INFO] GTDB search result was written to GCF_014640475.1_ASM1464047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:40,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:40,863] [INFO] DFAST_QC result json was written to GCF_014640475.1_ASM1464047v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:40,864] [INFO] DFAST_QC completed!
[2024-01-24 12:31:40,864] [INFO] Total running time: 0h1m48s