[2024-01-25 17:49:50,826] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference
[2024-01-25 17:49:52,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:52,002] [INFO] Task started: Prodigal
[2024-01-25 17:49:52,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg855e1f53-88f8-40a0-b2cd-f2974c86b233/GCF_014644515.1_ASM1464451v1_genomic.fna.gz | prodigal -d GCF_014644515.1_ASM1464451v1_genomic.fna/cds.fna -a GCF_014644515.1_ASM1464451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:03,965] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:03,965] [INFO] Task started: HMMsearch
[2024-01-25 17:50:03,965] [INFO] Running command: hmmsearch --tblout GCF_014644515.1_ASM1464451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference/reference_markers.hmm GCF_014644515.1_ASM1464451v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:04,235] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:04,235] [INFO] Found 6/6 markers.
[2024-01-25 17:50:04,274] [INFO] Query marker FASTA was written to GCF_014644515.1_ASM1464451v1_genomic.fna/markers.fasta
[2024-01-25 17:50:04,274] [INFO] Task started: Blastn
[2024-01-25 17:50:04,274] [INFO] Running command: blastn -query GCF_014644515.1_ASM1464451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference/reference_markers.fasta -out GCF_014644515.1_ASM1464451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:05,243] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:05,245] [INFO] Selected 15 target genomes.
[2024-01-25 17:50:05,245] [INFO] Target genome list was writen to GCF_014644515.1_ASM1464451v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:05,263] [INFO] Task started: fastANI
[2024-01-25 17:50:05,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg855e1f53-88f8-40a0-b2cd-f2974c86b233/GCF_014644515.1_ASM1464451v1_genomic.fna.gz --refList GCF_014644515.1_ASM1464451v1_genomic.fna/target_genomes.txt --output GCF_014644515.1_ASM1464451v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:18,425] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:18,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:18,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:18,435] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:18,435] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:50:18,435] [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
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	100.0	1392	1393	95	inconclusive
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	95.825	1275	1393	95	inconclusive
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	85.413	1064	1393	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	84.2882	995	1393	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	83.3154	921	1393	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	83.2001	928	1393	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	83.0804	935	1393	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	82.9956	927	1393	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	82.9894	928	1393	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	82.1525	808	1393	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	81.1767	634	1393	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.8262	349	1393	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.7445	419	1393	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.596	322	1393	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.5309	324	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:18,436] [INFO] DFAST Taxonomy check result was written to GCF_014644515.1_ASM1464451v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:18,437] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:18,437] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:18,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference/checkm_data
[2024-01-25 17:50:18,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:18,477] [INFO] Task started: CheckM
[2024-01-25 17:50:18,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644515.1_ASM1464451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644515.1_ASM1464451v1_genomic.fna/checkm_input GCF_014644515.1_ASM1464451v1_genomic.fna/checkm_result
[2024-01-25 17:50:54,300] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:54,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:54,314] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:54,315] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:54,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644515.1_ASM1464451v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:54,315] [INFO] Task started: Blastn
[2024-01-25 17:50:54,315] [INFO] Running command: blastn -query GCF_014644515.1_ASM1464451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41db1eb7-d7f6-46ef-8fad-c97eefff56c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644515.1_ASM1464451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:55,854] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:55,857] [INFO] Selected 11 target genomes.
[2024-01-25 17:50:55,857] [INFO] Target genome list was writen to GCF_014644515.1_ASM1464451v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:55,867] [INFO] Task started: fastANI
[2024-01-25 17:50:55,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg855e1f53-88f8-40a0-b2cd-f2974c86b233/GCF_014644515.1_ASM1464451v1_genomic.fna.gz --refList GCF_014644515.1_ASM1464451v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644515.1_ASM1464451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:07,805] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:07,812] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:07,812] [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_014644495.1	s__Pseudarthrobacter polychromogenes	95.825	1275	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	97.13	95.62	0.90	0.87	5	conclusive
GCF_013314975.1	s__Pseudarthrobacter oxydans	94.5761	1203	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641125.1	s__Pseudarthrobacter sp001641125	93.4644	1241	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741265.1	s__Pseudarthrobacter sp009741265	86.4532	1062	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002892835.1	s__Pseudarthrobacter sp002892835	86.4154	1084	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953935.1	s__Pseudarthrobacter sp002953935	86.1144	1034	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151685.1	s__Pseudarthrobacter sp006151685	86.0828	1035	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000189535.1	s__Pseudarthrobacter phenanthrenivorans	85.3963	1066	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.29	98.26	0.89	0.89	3	-
GCF_900537115.1	s__Pseudarthrobacter sp900537115	84.5746	1023	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168295.1	s__Pseudarthrobacter sp900168295	84.3129	1019	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.77	97.56	0.93	0.89	3	-
GCF_004320525.1	s__Pseudarthrobacter sp004320525	82.9171	904	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:07,814] [INFO] GTDB search result was written to GCF_014644515.1_ASM1464451v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:07,814] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:07,817] [INFO] DFAST_QC result json was written to GCF_014644515.1_ASM1464451v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:07,818] [INFO] DFAST_QC completed!
[2024-01-25 17:51:07,818] [INFO] Total running time: 0h1m17s