[2024-01-25 19:39:50,610] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:50,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:50,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference
[2024-01-25 19:39:51,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:51,756] [INFO] Task started: Prodigal
[2024-01-25 19:39:51,756] [INFO] Running command: gunzip -c /var/lib/cwl/stga69cda3c-eedd-4cbd-bc07-d3c1cdb60422/GCF_000496735.2_MKO1_genomic.fna.gz | prodigal -d GCF_000496735.2_MKO1_genomic.fna/cds.fna -a GCF_000496735.2_MKO1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:01,117] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:01,117] [INFO] Task started: HMMsearch
[2024-01-25 19:40:01,117] [INFO] Running command: hmmsearch --tblout GCF_000496735.2_MKO1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference/reference_markers.hmm GCF_000496735.2_MKO1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:01,336] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:01,338] [INFO] Found 6/6 markers.
[2024-01-25 19:40:01,370] [INFO] Query marker FASTA was written to GCF_000496735.2_MKO1_genomic.fna/markers.fasta
[2024-01-25 19:40:01,370] [INFO] Task started: Blastn
[2024-01-25 19:40:01,370] [INFO] Running command: blastn -query GCF_000496735.2_MKO1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference/reference_markers.fasta -out GCF_000496735.2_MKO1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:01,982] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:01,984] [INFO] Selected 25 target genomes.
[2024-01-25 19:40:01,985] [INFO] Target genome list was writen to GCF_000496735.2_MKO1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:02,005] [INFO] Task started: fastANI
[2024-01-25 19:40:02,005] [INFO] Running command: fastANI --query /var/lib/cwl/stga69cda3c-eedd-4cbd-bc07-d3c1cdb60422/GCF_000496735.2_MKO1_genomic.fna.gz --refList GCF_000496735.2_MKO1_genomic.fna/target_genomes.txt --output GCF_000496735.2_MKO1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:19,456] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:19,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:19,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:19,463] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:40:19,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:19,463] [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
Methyloglobulus morosus	strain=KoM1	GCA_000496735.2	1410681	1410681	type	True	100.0	1276	1284	95	conclusive
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.7284	98	1284	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	76.7166	91	1284	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	76.464	148	1284	95	below_threshold
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	76.1118	138	1284	95	below_threshold
Methylicorpusculum oleiharenae	strain=XLMV4	GCA_009828925.2	1338687	1338687	type	True	75.9985	72	1284	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	75.8546	60	1284	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	75.7496	68	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:19,465] [INFO] DFAST Taxonomy check result was written to GCF_000496735.2_MKO1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:19,465] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:19,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:19,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference/checkm_data
[2024-01-25 19:40:19,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:19,509] [INFO] Task started: CheckM
[2024-01-25 19:40:19,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000496735.2_MKO1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000496735.2_MKO1_genomic.fna/checkm_input GCF_000496735.2_MKO1_genomic.fna/checkm_result
[2024-01-25 19:40:51,170] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:51,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:51,188] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:51,188] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:51,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000496735.2_MKO1_genomic.fna/markers.fasta)
[2024-01-25 19:40:51,188] [INFO] Task started: Blastn
[2024-01-25 19:40:51,188] [INFO] Running command: blastn -query GCF_000496735.2_MKO1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ace5e6a-db94-4e2f-918a-da02770cc642/dqc_reference/reference_markers_gtdb.fasta -out GCF_000496735.2_MKO1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:52,251] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:52,254] [INFO] Selected 20 target genomes.
[2024-01-25 19:40:52,254] [INFO] Target genome list was writen to GCF_000496735.2_MKO1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:52,269] [INFO] Task started: fastANI
[2024-01-25 19:40:52,269] [INFO] Running command: fastANI --query /var/lib/cwl/stga69cda3c-eedd-4cbd-bc07-d3c1cdb60422/GCF_000496735.2_MKO1_genomic.fna.gz --refList GCF_000496735.2_MKO1_genomic.fna/target_genomes_gtdb.txt --output GCF_000496735.2_MKO1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:05,774] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:05,784] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:05,784] [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_000496735.2	s__Methyloglobulus morosus	100.0	1276	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009695535.1	s__Methyloglobulus sp009695535	79.1917	284	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140405.1	s__Methyloglobulus sp013140405	79.0788	358	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155565.1	s__Methyloglobulus sp003155565	78.9863	378	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141505.1	s__Methyloglobulus sp013141505	78.1316	331	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483425.1	s__Methyloglobulus sp002483425	77.2778	240	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190755.2	s__Methylobacter_A tundripaludum	76.4766	148	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	95.80	95.64	0.85	0.80	9	-
GCA_004299305.1	s__Methylobacter_A sp004299305	76.2765	119	1284	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_000384075.1	s__Methylovulum miyakonense	76.1362	136	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	96.67	96.67	0.87	0.87	2	-
GCA_903928685.1	s__Methylovulum sp903928685	76.1255	108	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	99.91	99.86	0.97	0.96	8	-
GCF_002934365.1	s__Methylobacter_A tundripaludum_A	76.1249	147	1284	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_003158415.1	s__KS41 sp003158415	76.1192	97	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994235.2	s__Methylobacter_A oryzae	76.1014	119	1284	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_013140465.1	s__KS41 sp013140465	76.0629	94	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903064715.1	s__Methylomonas sp903064715	75.8664	61	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903839795.1	s__KS41 sp903839795	75.7442	61	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:05,786] [INFO] GTDB search result was written to GCF_000496735.2_MKO1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:05,786] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:05,793] [INFO] DFAST_QC result json was written to GCF_000496735.2_MKO1_genomic.fna/dqc_result.json
[2024-01-25 19:41:05,793] [INFO] DFAST_QC completed!
[2024-01-25 19:41:05,793] [INFO] Total running time: 0h1m15s