[2024-01-24 12:39:35,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,167] [INFO] DQC Reference Directory: /var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference
[2024-01-24 12:39:36,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,483] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,483] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7ed3ac7-307f-4adf-bd89-8e10dcfd7af9/GCF_003584645.1_ASM358464v1_genomic.fna.gz | prodigal -d GCF_003584645.1_ASM358464v1_genomic.fna/cds.fna -a GCF_003584645.1_ASM358464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:55,839] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:55,839] [INFO] Task started: HMMsearch
[2024-01-24 12:39:55,839] [INFO] Running command: hmmsearch --tblout GCF_003584645.1_ASM358464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference/reference_markers.hmm GCF_003584645.1_ASM358464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:56,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:56,168] [INFO] Found 6/6 markers.
[2024-01-24 12:39:56,217] [INFO] Query marker FASTA was written to GCF_003584645.1_ASM358464v1_genomic.fna/markers.fasta
[2024-01-24 12:39:56,217] [INFO] Task started: Blastn
[2024-01-24 12:39:56,218] [INFO] Running command: blastn -query GCF_003584645.1_ASM358464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference/reference_markers.fasta -out GCF_003584645.1_ASM358464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:56,943] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:56,948] [INFO] Selected 23 target genomes.
[2024-01-24 12:39:56,948] [INFO] Target genome list was writen to GCF_003584645.1_ASM358464v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:56,959] [INFO] Task started: fastANI
[2024-01-24 12:39:56,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ed3ac7-307f-4adf-bd89-8e10dcfd7af9/GCF_003584645.1_ASM358464v1_genomic.fna.gz --refList GCF_003584645.1_ASM358464v1_genomic.fna/target_genomes.txt --output GCF_003584645.1_ASM358464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:14,329] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:14,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:14,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:14,352] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:14,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:14,353] [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
Methylocaldum marinum	strain=S8	GCA_003584645.1	1432792	1432792	type	True	100.0	2028	2029	95	conclusive
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	77.2827	182	2029	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	77.2589	214	2029	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	77.2426	189	2029	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.9841	181	2029	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	76.8852	112	2029	95	below_threshold
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	76.8682	178	2029	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.8473	78	2029	95	below_threshold
Methylotetracoccus oryzae	strain=C50C1	GCA_006175985.1	1919059	1919059	type	True	76.6859	129	2029	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.6495	51	2029	95	below_threshold
Chromohalobacter salexigens	strain=DSM 3043	GCA_000055785.1	158080	158080	type	True	76.6234	50	2029	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	76.4692	91	2029	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4239	66	2029	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	75.917	61	2029	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.7288	87	2029	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.5042	60	2029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:14,357] [INFO] DFAST Taxonomy check result was written to GCF_003584645.1_ASM358464v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:14,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:14,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:14,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference/checkm_data
[2024-01-24 12:40:14,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:14,429] [INFO] Task started: CheckM
[2024-01-24 12:40:14,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003584645.1_ASM358464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003584645.1_ASM358464v1_genomic.fna/checkm_input GCF_003584645.1_ASM358464v1_genomic.fna/checkm_result
[2024-01-24 12:41:10,301] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:10,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:10,329] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:10,329] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:10,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003584645.1_ASM358464v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:10,330] [INFO] Task started: Blastn
[2024-01-24 12:41:10,330] [INFO] Running command: blastn -query GCF_003584645.1_ASM358464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd05e3d3a-0248-4673-8904-481cdf97918e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003584645.1_ASM358464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:11,543] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:11,548] [INFO] Selected 15 target genomes.
[2024-01-24 12:41:11,548] [INFO] Target genome list was writen to GCF_003584645.1_ASM358464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:11,558] [INFO] Task started: fastANI
[2024-01-24 12:41:11,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ed3ac7-307f-4adf-bd89-8e10dcfd7af9/GCF_003584645.1_ASM358464v1_genomic.fna.gz --refList GCF_003584645.1_ASM358464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003584645.1_ASM358464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:26,017] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:26,033] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:26,033] [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_003584645.1	s__Methylocaldum marinum	100.0	2029	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002005105.1	s__Methylocaldum sp002005105	83.5207	1185	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	98.51	98.17	0.91	0.88	6	-
GCF_000427385.1	s__Methylocaldum szegediense	81.6048	935	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810705.1	s__CADDYU01 sp902810705	77.4718	240	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__CADDYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934725.1	s__Methyloterricola oryzae	77.2803	180	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476545.1	s__Methylobacter sp015476545	77.2221	86	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424685.1	s__Methylococcus capsulatus	77.211	191	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	99.39	98.77	0.98	0.95	3	-
GCF_012769535.1	s__Methylococcus sp012769535	77.1891	213	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155475.1	s__Methylomagnum ishizawai	77.0067	241	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106025.1	s__Methylococcus sp016106025	76.9348	169	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	76.6223	66	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527095.1	s__Methylomicrobium lacus	76.4282	92	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812445.1	s__CADDZF01 sp902812445	76.1364	105	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__CADDZF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012939995.1	s__Competibacter phosphatis	75.5439	68	2029	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:26,036] [INFO] GTDB search result was written to GCF_003584645.1_ASM358464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:26,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:26,041] [INFO] DFAST_QC result json was written to GCF_003584645.1_ASM358464v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:26,041] [INFO] DFAST_QC completed!
[2024-01-24 12:41:26,041] [INFO] Total running time: 0h1m51s