[2024-01-25 17:42:20,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference
[2024-01-25 17:42:21,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,704] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cbb35d0-778f-43ff-9c46-2421afb191d8/GCF_021919345.1_ASM2191934v1_genomic.fna.gz | prodigal -d GCF_021919345.1_ASM2191934v1_genomic.fna/cds.fna -a GCF_021919345.1_ASM2191934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:34,727] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:34,727] [INFO] Task started: HMMsearch
[2024-01-25 17:42:34,727] [INFO] Running command: hmmsearch --tblout GCF_021919345.1_ASM2191934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference/reference_markers.hmm GCF_021919345.1_ASM2191934v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:34,978] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:34,985] [INFO] Found 6/6 markers.
[2024-01-25 17:42:35,032] [INFO] Query marker FASTA was written to GCF_021919345.1_ASM2191934v1_genomic.fna/markers.fasta
[2024-01-25 17:42:35,033] [INFO] Task started: Blastn
[2024-01-25 17:42:35,033] [INFO] Running command: blastn -query GCF_021919345.1_ASM2191934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference/reference_markers.fasta -out GCF_021919345.1_ASM2191934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:35,957] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:35,966] [INFO] Selected 11 target genomes.
[2024-01-25 17:42:35,967] [INFO] Target genome list was writen to GCF_021919345.1_ASM2191934v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:35,967] [INFO] Task started: fastANI
[2024-01-25 17:42:35,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cbb35d0-778f-43ff-9c46-2421afb191d8/GCF_021919345.1_ASM2191934v1_genomic.fna.gz --refList GCF_021919345.1_ASM2191934v1_genomic.fna/target_genomes.txt --output GCF_021919345.1_ASM2191934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:45,967] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:45,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:45,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:45,975] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:42:45,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:45,976] [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
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	100.0	1490	1493	95	conclusive
Paenarthrobacter nicotinovorans	strain=DSM 420	GCA_017876445.1	29320	29320	suspected-type	True	99.9956	1488	1493	95	conclusive
Paenarthrobacter nicotinovorans	strain=JCM 3874	GCA_014648735.1	29320	29320	suspected-type	True	99.9761	1462	1493	95	conclusive
Paenarthrobacter histidinolovorans	strain=JCM 2520	GCA_014647595.1	43664	43664	type	True	90.6494	1269	1493	95	below_threshold
Paenarthrobacter aurescens	strain=NBRC 12136	GCA_006538985.1	43663	43663	type	True	83.6308	1010	1493	95	below_threshold
Paenarthrobacter ilicis	strain=DSM 20138	GCA_016907545.1	43665	43665	type	True	82.9371	946	1493	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.8215	722	1493	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	79.5341	472	1493	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.6828	283	1493	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.6027	282	1493	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.2499	282	1493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:45,977] [INFO] DFAST Taxonomy check result was written to GCF_021919345.1_ASM2191934v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:45,977] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:45,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:45,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference/checkm_data
[2024-01-25 17:42:45,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:46,022] [INFO] Task started: CheckM
[2024-01-25 17:42:46,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021919345.1_ASM2191934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021919345.1_ASM2191934v1_genomic.fna/checkm_input GCF_021919345.1_ASM2191934v1_genomic.fna/checkm_result
[2024-01-25 17:43:26,430] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:26,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:26,451] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:26,451] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:26,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021919345.1_ASM2191934v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:26,451] [INFO] Task started: Blastn
[2024-01-25 17:43:26,452] [INFO] Running command: blastn -query GCF_021919345.1_ASM2191934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0958d48-f9d7-4930-99f2-503b0535eb09/dqc_reference/reference_markers_gtdb.fasta -out GCF_021919345.1_ASM2191934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:27,947] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:27,950] [INFO] Selected 12 target genomes.
[2024-01-25 17:43:27,950] [INFO] Target genome list was writen to GCF_021919345.1_ASM2191934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:27,952] [INFO] Task started: fastANI
[2024-01-25 17:43:27,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cbb35d0-778f-43ff-9c46-2421afb191d8/GCF_021919345.1_ASM2191934v1_genomic.fna.gz --refList GCF_021919345.1_ASM2191934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021919345.1_ASM2191934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:40,851] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:40,859] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:40,860] [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_014648735.1	s__Paenarthrobacter nicotinovorans	99.9761	1462	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.78	98.50	0.92	0.90	10	conclusive
GCF_014647595.1	s__Paenarthrobacter histidinolovorans	90.6494	1269	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786235.1	s__Paenarthrobacter nitroguajacolicus_A	86.062	1119	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007670255.1	s__Paenarthrobacter nicotinovorans_B	85.9171	1135	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014925.1	s__Paenarthrobacter aurescens_A	84.5758	1105	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.88	98.80	0.86	0.86	3	-
GCF_902706295.1	s__Paenarthrobacter sp902706295	84.5663	1094	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224285.1	s__Paenarthrobacter sp002224285	84.4337	1077	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106835.1	s__Paenarthrobacter sp900106835	84.3909	1089	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.81	98.81	0.92	0.92	2	-
GCF_018215265.1	s__Paenarthrobacter sp018215265	84.3574	1044	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979775.1	s__Paenarthrobacter sp002979775	84.2678	1057	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013179505.1	s__Paenarthrobacter sp013179505	84.0845	921	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907545.1	s__Paenarthrobacter ilicis	82.9125	945	1493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:40,862] [INFO] GTDB search result was written to GCF_021919345.1_ASM2191934v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:40,863] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:40,866] [INFO] DFAST_QC result json was written to GCF_021919345.1_ASM2191934v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:40,866] [INFO] DFAST_QC completed!
[2024-01-25 17:43:40,866] [INFO] Total running time: 0h1m20s