[2024-01-24 14:19:46,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference
[2024-01-24 14:19:48,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:48,162] [INFO] Task started: Prodigal
[2024-01-24 14:19:48,162] [INFO] Running command: gunzip -c /var/lib/cwl/stg1226be43-0c95-4355-aa12-5244489d881e/GCF_003667575.1_ASM366757v1_genomic.fna.gz | prodigal -d GCF_003667575.1_ASM366757v1_genomic.fna/cds.fna -a GCF_003667575.1_ASM366757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:00,516] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:00,516] [INFO] Task started: HMMsearch
[2024-01-24 14:20:00,516] [INFO] Running command: hmmsearch --tblout GCF_003667575.1_ASM366757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference/reference_markers.hmm GCF_003667575.1_ASM366757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:00,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:00,765] [INFO] Found 6/6 markers.
[2024-01-24 14:20:00,799] [INFO] Query marker FASTA was written to GCF_003667575.1_ASM366757v1_genomic.fna/markers.fasta
[2024-01-24 14:20:00,799] [INFO] Task started: Blastn
[2024-01-24 14:20:00,800] [INFO] Running command: blastn -query GCF_003667575.1_ASM366757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference/reference_markers.fasta -out GCF_003667575.1_ASM366757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:02,016] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:02,021] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:02,022] [INFO] Target genome list was writen to GCF_003667575.1_ASM366757v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:02,039] [INFO] Task started: fastANI
[2024-01-24 14:20:02,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg1226be43-0c95-4355-aa12-5244489d881e/GCF_003667575.1_ASM366757v1_genomic.fna.gz --refList GCF_003667575.1_ASM366757v1_genomic.fna/target_genomes.txt --output GCF_003667575.1_ASM366757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:12,367] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:12,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:12,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:12,382] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:12,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:12,383] [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
Mycetocola lacteus	strain=JCM 11654	GCA_003667575.1	76637	76637	type	True	100.0	1210	1267	95	conclusive
Mycetocola saprophilus	strain=NRRL B-24119	GCA_000718085.1	76636	76636	type	True	92.7128	969	1267	95	below_threshold
Mycetocola spongiae	strain=MSC19	GCA_020424085.1	2859226	2859226	type	True	79.7621	461	1267	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	78.2097	290	1267	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	78.159	281	1267	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	78.0947	202	1267	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.0373	260	1267	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	77.8242	215	1267	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	77.7963	251	1267	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	77.7034	260	1267	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	77.6946	278	1267	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	77.5295	232	1267	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	77.3571	211	1267	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.259	215	1267	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.1201	203	1267	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	77.091	205	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:12,403] [INFO] DFAST Taxonomy check result was written to GCF_003667575.1_ASM366757v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:12,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:12,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:12,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference/checkm_data
[2024-01-24 14:20:12,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:12,445] [INFO] Task started: CheckM
[2024-01-24 14:20:12,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667575.1_ASM366757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667575.1_ASM366757v1_genomic.fna/checkm_input GCF_003667575.1_ASM366757v1_genomic.fna/checkm_result
[2024-01-24 14:20:48,917] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:48,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:48,936] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:48,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:48,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667575.1_ASM366757v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:48,937] [INFO] Task started: Blastn
[2024-01-24 14:20:48,937] [INFO] Running command: blastn -query GCF_003667575.1_ASM366757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57827aa0-eddf-4924-a34e-55ed72ccd0ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667575.1_ASM366757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:50,811] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:50,815] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:50,815] [INFO] Target genome list was writen to GCF_003667575.1_ASM366757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:50,842] [INFO] Task started: fastANI
[2024-01-24 14:20:50,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg1226be43-0c95-4355-aa12-5244489d881e/GCF_003667575.1_ASM366757v1_genomic.fna.gz --refList GCF_003667575.1_ASM366757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003667575.1_ASM366757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:00,962] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:00,975] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:00,975] [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_003667575.1	s__Mycetocola lacteus	100.0	1200	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000718085.1	s__Mycetocola saprophilus	92.7128	969	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	98.52	97.04	0.95	0.91	3	-
GCF_003667565.1	s__Mycetocola tolaasinivorans	84.7112	786	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002936985.1	s__Microterricola pindariensis	78.1971	291	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_900104895.1	s__Microterricola viridarii	78.1331	283	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	78.0241	261	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984125.1	s__Okibacterium sp001984125	77.9739	243	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542775.1	s__Microterricola viridarii_A	77.9353	269	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425085.1	s__Microterricola sp001425085	77.8971	253	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	77.6908	261	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_003185895.1	s__Cryobacterium arcticum	77.6761	279	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758255.1	s__Microbacterium sp009758255	77.643	214	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428745.1	s__Leifsonia sp001428745	77.6307	233	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012317045.1	s__Leifsonia sp002105485	77.5888	260	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_001280205.1	s__Clavibacter capsici	77.403	184	1267	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:00,977] [INFO] GTDB search result was written to GCF_003667575.1_ASM366757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:00,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:00,981] [INFO] DFAST_QC result json was written to GCF_003667575.1_ASM366757v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:00,981] [INFO] DFAST_QC completed!
[2024-01-24 14:21:00,981] [INFO] Total running time: 0h1m14s