[2024-01-24 13:30:11,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:11,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:11,089] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference
[2024-01-24 13:30:12,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:12,362] [INFO] Task started: Prodigal
[2024-01-24 13:30:12,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d937e33-d8b2-41d0-b9ef-9a5612946612/GCF_000190755.2_ASM19075v3_genomic.fna.gz | prodigal -d GCF_000190755.2_ASM19075v3_genomic.fna/cds.fna -a GCF_000190755.2_ASM19075v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:25,658] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:25,658] [INFO] Task started: HMMsearch
[2024-01-24 13:30:25,658] [INFO] Running command: hmmsearch --tblout GCF_000190755.2_ASM19075v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference/reference_markers.hmm GCF_000190755.2_ASM19075v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:26,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:26,018] [INFO] Found 6/6 markers.
[2024-01-24 13:30:26,062] [INFO] Query marker FASTA was written to GCF_000190755.2_ASM19075v3_genomic.fna/markers.fasta
[2024-01-24 13:30:26,062] [INFO] Task started: Blastn
[2024-01-24 13:30:26,062] [INFO] Running command: blastn -query GCF_000190755.2_ASM19075v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference/reference_markers.fasta -out GCF_000190755.2_ASM19075v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:26,835] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:26,839] [INFO] Selected 24 target genomes.
[2024-01-24 13:30:26,839] [INFO] Target genome list was writen to GCF_000190755.2_ASM19075v3_genomic.fna/target_genomes.txt
[2024-01-24 13:30:26,882] [INFO] Task started: fastANI
[2024-01-24 13:30:26,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d937e33-d8b2-41d0-b9ef-9a5612946612/GCF_000190755.2_ASM19075v3_genomic.fna.gz --refList GCF_000190755.2_ASM19075v3_genomic.fna/target_genomes.txt --output GCF_000190755.2_ASM19075v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:47,158] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:47,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:47,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:47,169] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:30:47,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:47,169] [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
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	100.0	1614	1614	95	conclusive
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.9014	409	1614	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	77.84	179	1614	95	below_threshold
Methyloprofundus sedimenti	strain=WF1	GCA_002072955.1	1420851	1420851	type	True	77.5216	54	1614	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	77.518	263	1614	95	below_threshold
Methylotuvimicrobium alcaliphilum	strain=20Z	GCA_000968535.1	271065	271065	type	True	77.3073	147	1614	95	below_threshold
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	77.1527	234	1614	95	below_threshold
Methylovulum psychrotolerans	strain=Sph1	GCA_002923755.1	1704499	1704499	type	True	77.0961	210	1614	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	76.9538	211	1614	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	76.8726	130	1614	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.6797	143	1614	95	below_threshold
Methyloglobulus morosus	strain=KoM1	GCA_000496735.2	1410681	1410681	type	True	76.5393	151	1614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:47,171] [INFO] DFAST Taxonomy check result was written to GCF_000190755.2_ASM19075v3_genomic.fna/tc_result.tsv
[2024-01-24 13:30:47,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:47,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:47,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference/checkm_data
[2024-01-24 13:30:47,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:47,224] [INFO] Task started: CheckM
[2024-01-24 13:30:47,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000190755.2_ASM19075v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000190755.2_ASM19075v3_genomic.fna/checkm_input GCF_000190755.2_ASM19075v3_genomic.fna/checkm_result
[2024-01-24 13:31:28,923] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:28,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:28,947] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:28,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:28,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000190755.2_ASM19075v3_genomic.fna/markers.fasta)
[2024-01-24 13:31:28,949] [INFO] Task started: Blastn
[2024-01-24 13:31:28,949] [INFO] Running command: blastn -query GCF_000190755.2_ASM19075v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb68015f-86d6-4908-8518-6121993bafc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000190755.2_ASM19075v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:30,143] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:30,148] [INFO] Selected 7 target genomes.
[2024-01-24 13:31:30,148] [INFO] Target genome list was writen to GCF_000190755.2_ASM19075v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:30,161] [INFO] Task started: fastANI
[2024-01-24 13:31:30,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d937e33-d8b2-41d0-b9ef-9a5612946612/GCF_000190755.2_ASM19075v3_genomic.fna.gz --refList GCF_000190755.2_ASM19075v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000190755.2_ASM19075v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:39,896] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:39,903] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:39,903] [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_000190755.2	s__Methylobacter_A tundripaludum	100.0	1614	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	95.80	95.64	0.85	0.80	9	conclusive
GCF_002934365.1	s__Methylobacter_A tundripaludum_A	84.8762	966	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299305.1	s__Methylobacter_A sp004299305	84.4136	872	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322395.1	s__Methylobacter_A sp004322395	83.9127	939	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784875.1	s__Methylobacter_A sp016784875	82.6698	590	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994235.2	s__Methylobacter_A oryzae	81.7551	940	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832775.1	s__Methylobacter_A sp903832775	79.2513	473	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	99.74	99.60	0.93	0.90	13	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:39,905] [INFO] GTDB search result was written to GCF_000190755.2_ASM19075v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:39,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:39,909] [INFO] DFAST_QC result json was written to GCF_000190755.2_ASM19075v3_genomic.fna/dqc_result.json
[2024-01-24 13:31:39,909] [INFO] DFAST_QC completed!
[2024-01-24 13:31:39,909] [INFO] Total running time: 0h1m29s