[2024-01-24 14:32:34,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:34,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:34,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference
[2024-01-24 14:32:35,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:35,417] [INFO] Task started: Prodigal
[2024-01-24 14:32:35,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg17ca5b01-e3ad-4a38-990a-3d021d052406/GCF_003369445.1_ASM336944v1_genomic.fna.gz | prodigal -d GCF_003369445.1_ASM336944v1_genomic.fna/cds.fna -a GCF_003369445.1_ASM336944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:49,052] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:49,052] [INFO] Task started: HMMsearch
[2024-01-24 14:32:49,052] [INFO] Running command: hmmsearch --tblout GCF_003369445.1_ASM336944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference/reference_markers.hmm GCF_003369445.1_ASM336944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:49,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:49,342] [INFO] Found 6/6 markers.
[2024-01-24 14:32:49,382] [INFO] Query marker FASTA was written to GCF_003369445.1_ASM336944v1_genomic.fna/markers.fasta
[2024-01-24 14:32:49,383] [INFO] Task started: Blastn
[2024-01-24 14:32:49,383] [INFO] Running command: blastn -query GCF_003369445.1_ASM336944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference/reference_markers.fasta -out GCF_003369445.1_ASM336944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:50,480] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:50,484] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:50,484] [INFO] Target genome list was writen to GCF_003369445.1_ASM336944v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:50,489] [INFO] Task started: fastANI
[2024-01-24 14:32:50,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ca5b01-e3ad-4a38-990a-3d021d052406/GCF_003369445.1_ASM336944v1_genomic.fna.gz --refList GCF_003369445.1_ASM336944v1_genomic.fna/target_genomes.txt --output GCF_003369445.1_ASM336944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:03,089] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:03,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:03,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:03,106] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:33:03,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:33:03,107] [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
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	100.0	1411	1412	95	conclusive
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	91.2592	1145	1412	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	88.9862	1104	1412	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	88.9694	1119	1412	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	80.9459	681	1412	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	80.8804	712	1412	95	below_threshold
Arthrobacter terricola	strain=JH1-1	GCA_004354015.1	2547396	2547396	type	True	80.8619	697	1412	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.7841	686	1412	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	80.7522	655	1412	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	80.6368	652	1412	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	79.669	491	1412	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.997	434	1412	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.5882	373	1412	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.5749	377	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:03,108] [INFO] DFAST Taxonomy check result was written to GCF_003369445.1_ASM336944v1_genomic.fna/tc_result.tsv
[2024-01-24 14:33:03,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:03,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:03,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference/checkm_data
[2024-01-24 14:33:03,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:03,150] [INFO] Task started: CheckM
[2024-01-24 14:33:03,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003369445.1_ASM336944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003369445.1_ASM336944v1_genomic.fna/checkm_input GCF_003369445.1_ASM336944v1_genomic.fna/checkm_result
[2024-01-24 14:33:43,047] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:43,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:43,072] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:43,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:43,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003369445.1_ASM336944v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:43,073] [INFO] Task started: Blastn
[2024-01-24 14:33:43,073] [INFO] Running command: blastn -query GCF_003369445.1_ASM336944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc10fa6-ea15-43fe-87d9-67098faa1d96/dqc_reference/reference_markers_gtdb.fasta -out GCF_003369445.1_ASM336944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:44,776] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:44,781] [INFO] Selected 8 target genomes.
[2024-01-24 14:33:44,781] [INFO] Target genome list was writen to GCF_003369445.1_ASM336944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:44,829] [INFO] Task started: fastANI
[2024-01-24 14:33:44,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ca5b01-e3ad-4a38-990a-3d021d052406/GCF_003369445.1_ASM336944v1_genomic.fna.gz --refList GCF_003369445.1_ASM336944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003369445.1_ASM336944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:54,166] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:54,181] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:54,182] [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_003369445.1	s__Arthrobacter_G silvisoli	100.0	1411	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003614925.1	s__Arthrobacter_G celericrescens	91.2483	1146	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	88.9908	1103	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	86.3005	1004	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017368795.1	s__PO-11 sp017368795	82.3104	773	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969265.1	s__Arthrobacter sp001969265	81.0459	722	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	98.26	98.26	0.90	0.90	2	-
GCF_004320525.1	s__Pseudarthrobacter sp004320525	80.8088	703	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007670255.1	s__Paenarthrobacter nicotinovorans_B	80.5469	680	1412	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:54,184] [INFO] GTDB search result was written to GCF_003369445.1_ASM336944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:54,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:54,190] [INFO] DFAST_QC result json was written to GCF_003369445.1_ASM336944v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:54,190] [INFO] DFAST_QC completed!
[2024-01-24 14:33:54,190] [INFO] Total running time: 0h1m20s