[2024-01-24 13:21:11,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference
[2024-01-24 13:21:12,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,363] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fdbe891-21d5-4ead-a41c-83afd25639ab/GCF_009828925.2_ASM982892v2_genomic.fna.gz | prodigal -d GCF_009828925.2_ASM982892v2_genomic.fna/cds.fna -a GCF_009828925.2_ASM982892v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:32,698] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:32,699] [INFO] Task started: HMMsearch
[2024-01-24 13:21:32,699] [INFO] Running command: hmmsearch --tblout GCF_009828925.2_ASM982892v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference/reference_markers.hmm GCF_009828925.2_ASM982892v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:33,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:33,019] [INFO] Found 6/6 markers.
[2024-01-24 13:21:33,069] [INFO] Query marker FASTA was written to GCF_009828925.2_ASM982892v2_genomic.fna/markers.fasta
[2024-01-24 13:21:33,069] [INFO] Task started: Blastn
[2024-01-24 13:21:33,069] [INFO] Running command: blastn -query GCF_009828925.2_ASM982892v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference/reference_markers.fasta -out GCF_009828925.2_ASM982892v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:33,716] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:33,721] [INFO] Selected 30 target genomes.
[2024-01-24 13:21:33,721] [INFO] Target genome list was writen to GCF_009828925.2_ASM982892v2_genomic.fna/target_genomes.txt
[2024-01-24 13:21:33,739] [INFO] Task started: fastANI
[2024-01-24 13:21:33,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fdbe891-21d5-4ead-a41c-83afd25639ab/GCF_009828925.2_ASM982892v2_genomic.fna.gz --refList GCF_009828925.2_ASM982892v2_genomic.fna/target_genomes.txt --output GCF_009828925.2_ASM982892v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:54,397] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:54,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:54,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:54,407] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:54,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:54,408] [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
Methylicorpusculum oleiharenae	strain=XLMV4	GCA_009828925.2	1338687	1338687	type	True	100.0	1942	1948	95	conclusive
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	81.7878	163	1948	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	77.5481	96	1948	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	77.298	150	1948	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	77.274	86	1948	95	below_threshold
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	77.1657	101	1948	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.127	152	1948	95	below_threshold
Methylocucumis oryzae	strain=Sn10-6	GCA_000963695.1	1632867	1632867	type	True	76.2333	67	1948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:54,409] [INFO] DFAST Taxonomy check result was written to GCF_009828925.2_ASM982892v2_genomic.fna/tc_result.tsv
[2024-01-24 13:21:54,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:54,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:54,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference/checkm_data
[2024-01-24 13:21:54,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:54,474] [INFO] Task started: CheckM
[2024-01-24 13:21:54,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828925.2_ASM982892v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828925.2_ASM982892v2_genomic.fna/checkm_input GCF_009828925.2_ASM982892v2_genomic.fna/checkm_result
[2024-01-24 13:22:57,655] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:57,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:57,680] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:57,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:57,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828925.2_ASM982892v2_genomic.fna/markers.fasta)
[2024-01-24 13:22:57,681] [INFO] Task started: Blastn
[2024-01-24 13:22:57,681] [INFO] Running command: blastn -query GCF_009828925.2_ASM982892v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg84aa3912-5c85-4cf8-a779-a5e6e9d8414a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828925.2_ASM982892v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:58,699] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:58,704] [INFO] Selected 20 target genomes.
[2024-01-24 13:22:58,704] [INFO] Target genome list was writen to GCF_009828925.2_ASM982892v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:58,750] [INFO] Task started: fastANI
[2024-01-24 13:22:58,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fdbe891-21d5-4ead-a41c-83afd25639ab/GCF_009828925.2_ASM982892v2_genomic.fna.gz --refList GCF_009828925.2_ASM982892v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009828925.2_ASM982892v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:13,459] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:13,476] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:13,476] [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_009828925.1	s__Methylicorpusculum oleiharenae	99.9212	1789	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylicorpusculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018333785.1	s__Methylicorpusculum sp018333785	93.1035	1248	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylicorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002928965.1	s__Methylomonas sp002928965	78.0834	131	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006788925.1	s__Methylotuvimicrobium kenyense	77.8254	217	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843155.1	s__PGZD01 sp002843155	77.7398	177	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__PGZD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733935.1	s__Methylomarinum vadi	77.4383	86	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomarinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018734325.1	s__Methylomonas paludis	77.3787	91	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.09	98.96	0.96	0.94	4	-
GCF_000384075.1	s__Methylovulum miyakonense	77.2261	102	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	96.67	96.67	0.87	0.87	2	-
GCA_007135635.1	s__Methylotuvimicrobium sp007135635	77.0662	104	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005239965.1	s__Crenothrix sp005239965	76.8372	78	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Crenothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003584865.1	s__KS41 sp003584865	76.6287	50	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	97.03	0.84	0.75	9	-
GCA_004299305.1	s__Methylobacter_A sp004299305	76.5501	116	1948	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_002934365.1	s__Methylobacter_A tundripaludum_A	76.5314	137	1948	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_003584895.1	s__KS41 sp003584895	76.4211	52	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.75	98.03	0.85	0.79	12	-
GCA_003158415.1	s__KS41 sp003158415	76.3564	92	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140405.1	s__Methyloglobulus sp013140405	76.071	54	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839795.1	s__KS41 sp903839795	75.9472	74	1948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:13,478] [INFO] GTDB search result was written to GCF_009828925.2_ASM982892v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:13,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:13,481] [INFO] DFAST_QC result json was written to GCF_009828925.2_ASM982892v2_genomic.fna/dqc_result.json
[2024-01-24 13:23:13,482] [INFO] DFAST_QC completed!
[2024-01-24 13:23:13,482] [INFO] Total running time: 0h2m2s