[2024-01-24 14:54:55,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:55,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:55,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference
[2024-01-24 14:54:56,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:56,565] [INFO] Task started: Prodigal
[2024-01-24 14:54:56,565] [INFO] Running command: gunzip -c /var/lib/cwl/stgf29dfcdf-4ff4-42e5-8443-038231ac6290/GCF_003634095.1_ASM363409v1_genomic.fna.gz | prodigal -d GCF_003634095.1_ASM363409v1_genomic.fna/cds.fna -a GCF_003634095.1_ASM363409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:10,045] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:10,046] [INFO] Task started: HMMsearch
[2024-01-24 14:55:10,046] [INFO] Running command: hmmsearch --tblout GCF_003634095.1_ASM363409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference/reference_markers.hmm GCF_003634095.1_ASM363409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:10,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:10,367] [INFO] Found 6/6 markers.
[2024-01-24 14:55:10,405] [INFO] Query marker FASTA was written to GCF_003634095.1_ASM363409v1_genomic.fna/markers.fasta
[2024-01-24 14:55:10,406] [INFO] Task started: Blastn
[2024-01-24 14:55:10,406] [INFO] Running command: blastn -query GCF_003634095.1_ASM363409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference/reference_markers.fasta -out GCF_003634095.1_ASM363409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:11,638] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:11,642] [INFO] Selected 20 target genomes.
[2024-01-24 14:55:11,642] [INFO] Target genome list was writen to GCF_003634095.1_ASM363409v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:11,652] [INFO] Task started: fastANI
[2024-01-24 14:55:11,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29dfcdf-4ff4-42e5-8443-038231ac6290/GCF_003634095.1_ASM363409v1_genomic.fna.gz --refList GCF_003634095.1_ASM363409v1_genomic.fna/target_genomes.txt --output GCF_003634095.1_ASM363409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:32,067] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:32,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:32,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:32,084] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:32,084] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:32,084] [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 pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	81.6189	708	1426	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	81.5631	731	1426	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	81.5349	710	1426	95	below_threshold
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	81.4452	734	1426	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	81.3465	705	1426	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	81.2369	651	1426	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	81.1946	637	1426	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	81.0524	658	1426	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	81.0297	639	1426	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	81.0151	676	1426	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.9817	633	1426	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	80.8282	632	1426	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	80.8256	710	1426	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	80.7825	630	1426	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	80.7327	713	1426	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	80.0829	528	1426	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	79.9573	545	1426	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.9037	444	1426	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.7553	383	1426	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.6937	396	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:32,086] [INFO] DFAST Taxonomy check result was written to GCF_003634095.1_ASM363409v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:32,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:32,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:32,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference/checkm_data
[2024-01-24 14:55:32,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:32,129] [INFO] Task started: CheckM
[2024-01-24 14:55:32,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634095.1_ASM363409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634095.1_ASM363409v1_genomic.fna/checkm_input GCF_003634095.1_ASM363409v1_genomic.fna/checkm_result
[2024-01-24 14:56:11,757] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:11,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:11,780] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:11,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:11,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634095.1_ASM363409v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:11,781] [INFO] Task started: Blastn
[2024-01-24 14:56:11,781] [INFO] Running command: blastn -query GCF_003634095.1_ASM363409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f2f776-471b-4d54-ba5f-0ce76ef0367c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634095.1_ASM363409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:13,481] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:13,484] [INFO] Selected 8 target genomes.
[2024-01-24 14:56:13,484] [INFO] Target genome list was writen to GCF_003634095.1_ASM363409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:13,489] [INFO] Task started: fastANI
[2024-01-24 14:56:13,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29dfcdf-4ff4-42e5-8443-038231ac6290/GCF_003634095.1_ASM363409v1_genomic.fna.gz --refList GCF_003634095.1_ASM363409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634095.1_ASM363409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:22,435] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:22,442] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:22,443] [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_003634095.1	s__Arthrobacter_I oryzae	100.0	1424	1426	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003097355.1	s__Arthrobacter_I sp003097355	88.2236	1152	1426	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	95.72	95.72	0.82	0.82	2	-
GCF_900102895.1	s__Arthrobacter_I sp900102895	88.1089	1070	1426	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_900102785.1	s__Arthrobacter_I sp900102785	88.0211	1090	1426	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_000374925.1	s__Arthrobacter_I sp000374925	87.9733	1116	1426	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	97.54	97.54	0.90	0.90	2	-
GCF_900168135.1	s__Arthrobacter_I sp900168135	87.6026	1117	1426	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	95.10	95.10	0.85	0.85	2	-
GCF_003352915.1	s__Arthrobacter_I sp003352915	86.6288	1082	1426	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_900116495.1	s__Arthrobacter_I sp900116495	86.3138	1032	1426	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:22,444] [INFO] GTDB search result was written to GCF_003634095.1_ASM363409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:22,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:22,448] [INFO] DFAST_QC result json was written to GCF_003634095.1_ASM363409v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:22,448] [INFO] DFAST_QC completed!
[2024-01-24 14:56:22,449] [INFO] Total running time: 0h1m27s