[2024-01-24 13:12:53,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:53,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:53,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference
[2024-01-24 13:12:55,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:55,122] [INFO] Task started: Prodigal
[2024-01-24 13:12:55,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a4591ef-ce2c-4177-9c66-d21251247c14/GCF_003614925.1_ASM361492v1_genomic.fna.gz | prodigal -d GCF_003614925.1_ASM361492v1_genomic.fna/cds.fna -a GCF_003614925.1_ASM361492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:08,919] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:08,920] [INFO] Task started: HMMsearch
[2024-01-24 13:13:08,920] [INFO] Running command: hmmsearch --tblout GCF_003614925.1_ASM361492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference/reference_markers.hmm GCF_003614925.1_ASM361492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:09,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:09,205] [INFO] Found 6/6 markers.
[2024-01-24 13:13:09,247] [INFO] Query marker FASTA was written to GCF_003614925.1_ASM361492v1_genomic.fna/markers.fasta
[2024-01-24 13:13:09,248] [INFO] Task started: Blastn
[2024-01-24 13:13:09,248] [INFO] Running command: blastn -query GCF_003614925.1_ASM361492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference/reference_markers.fasta -out GCF_003614925.1_ASM361492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:10,375] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:10,378] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:10,379] [INFO] Target genome list was writen to GCF_003614925.1_ASM361492v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:10,401] [INFO] Task started: fastANI
[2024-01-24 13:13:10,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4591ef-ce2c-4177-9c66-d21251247c14/GCF_003614925.1_ASM361492v1_genomic.fna.gz --refList GCF_003614925.1_ASM361492v1_genomic.fna/target_genomes.txt --output GCF_003614925.1_ASM361492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:22,942] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:22,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:22,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:22,958] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:22,958] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:22,958] [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 celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	100.0	1431	1435	95	conclusive
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	91.1856	1171	1435	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	90.3024	1170	1435	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	90.2279	1182	1435	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	81.2955	710	1435	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	80.9897	650	1435	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	80.9533	704	1435	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.9103	703	1435	95	below_threshold
Arthrobacter terricola	strain=JH1-1	GCA_004354015.1	2547396	2547396	type	True	80.9047	740	1435	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	79.8832	508	1435	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	79.3003	481	1435	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	79.0604	375	1435	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	79.0037	377	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:22,960] [INFO] DFAST Taxonomy check result was written to GCF_003614925.1_ASM361492v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:22,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:22,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:22,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference/checkm_data
[2024-01-24 13:13:22,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:23,005] [INFO] Task started: CheckM
[2024-01-24 13:13:23,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003614925.1_ASM361492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003614925.1_ASM361492v1_genomic.fna/checkm_input GCF_003614925.1_ASM361492v1_genomic.fna/checkm_result
[2024-01-24 13:14:03,849] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:03,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:03,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:03,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003614925.1_ASM361492v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:03,867] [INFO] Task started: Blastn
[2024-01-24 13:14:03,867] [INFO] Running command: blastn -query GCF_003614925.1_ASM361492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06129cce-0d9c-4850-81d8-5abaed9b46d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003614925.1_ASM361492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:05,624] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:05,628] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:05,628] [INFO] Target genome list was writen to GCF_003614925.1_ASM361492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:05,637] [INFO] Task started: fastANI
[2024-01-24 13:14:05,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4591ef-ce2c-4177-9c66-d21251247c14/GCF_003614925.1_ASM361492v1_genomic.fna.gz --refList GCF_003614925.1_ASM361492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003614925.1_ASM361492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:13,816] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,828] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:13,828] [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_003614925.1	s__Arthrobacter_G celericrescens	100.0	1431	1435	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_003369445.1	s__Arthrobacter_G silvisoli	91.1878	1171	1435	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	90.2088	1183	1435	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	86.6646	1042	1435	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	82.581	783	1435	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_001422645.1	s__Arthrobacter_I sp001422645	81.0333	678	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018215265.1	s__Paenarthrobacter sp018215265	80.8867	690	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613855.1	s__ISL-30 sp018613855	80.6062	616	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__ISL-30	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,830] [INFO] GTDB search result was written to GCF_003614925.1_ASM361492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:13,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:13,834] [INFO] DFAST_QC result json was written to GCF_003614925.1_ASM361492v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:13,834] [INFO] DFAST_QC completed!
[2024-01-24 13:14:13,835] [INFO] Total running time: 0h1m20s