[2023-06-13 15:12:34,394] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:12:34,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:12:34,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference
[2023-06-13 15:12:35,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:12:35,720] [INFO] Task started: Prodigal
[2023-06-13 15:12:35,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da79bea-881e-44ea-8a0f-08b080c24f77/GCA_947484175.1_TH-Jun18-130_genomic.fna.gz | prodigal -d GCA_947484175.1_TH-Jun18-130_genomic.fna/cds.fna -a GCA_947484175.1_TH-Jun18-130_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:12:48,794] [INFO] Task succeeded: Prodigal
[2023-06-13 15:12:48,795] [INFO] Task started: HMMsearch
[2023-06-13 15:12:48,795] [INFO] Running command: hmmsearch --tblout GCA_947484175.1_TH-Jun18-130_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference/reference_markers.hmm GCA_947484175.1_TH-Jun18-130_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:12:49,106] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:12:49,109] [INFO] Found 6/6 markers.
[2023-06-13 15:12:49,171] [INFO] Query marker FASTA was written to GCA_947484175.1_TH-Jun18-130_genomic.fna/markers.fasta
[2023-06-13 15:12:49,172] [INFO] Task started: Blastn
[2023-06-13 15:12:49,172] [INFO] Running command: blastn -query GCA_947484175.1_TH-Jun18-130_genomic.fna/markers.fasta -db /var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference/reference_markers.fasta -out GCA_947484175.1_TH-Jun18-130_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:12:49,826] [INFO] Task succeeded: Blastn
[2023-06-13 15:12:49,831] [INFO] Selected 35 target genomes.
[2023-06-13 15:12:49,831] [INFO] Target genome list was writen to GCA_947484175.1_TH-Jun18-130_genomic.fna/target_genomes.txt
[2023-06-13 15:12:49,838] [INFO] Task started: fastANI
[2023-06-13 15:12:49,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da79bea-881e-44ea-8a0f-08b080c24f77/GCA_947484175.1_TH-Jun18-130_genomic.fna.gz --refList GCA_947484175.1_TH-Jun18-130_genomic.fna/target_genomes.txt --output GCA_947484175.1_TH-Jun18-130_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:13:22,503] [INFO] Task succeeded: fastANI
[2023-06-13 15:13:22,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:13:22,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:13:22,525] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:13:22,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:13:22,526] [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
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	74.9308	58	1370	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	74.9146	71	1370	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	74.906	78	1370	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8754	218	1370	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	74.8669	65	1370	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.8516	63	1370	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	74.8344	84	1370	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8197	212	1370	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	74.8024	84	1370	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.7957	177	1370	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.7759	83	1370	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	74.7484	61	1370	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.7313	64	1370	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	74.73	63	1370	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	74.7169	106	1370	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	74.7138	61	1370	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	74.705	63	1370	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	74.6812	62	1370	95	below_threshold
Burkholderia lata	strain=383	GCA_000012945.1	482957	482957	suspected-type	True	74.6707	75	1370	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	74.6494	57	1370	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	74.611	61	1370	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	74.5732	67	1370	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:13:22,528] [INFO] DFAST Taxonomy check result was written to GCA_947484175.1_TH-Jun18-130_genomic.fna/tc_result.tsv
[2023-06-13 15:13:22,528] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:13:22,528] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:13:22,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference/checkm_data
[2023-06-13 15:13:22,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:13:22,578] [INFO] Task started: CheckM
[2023-06-13 15:13:22,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947484175.1_TH-Jun18-130_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947484175.1_TH-Jun18-130_genomic.fna/checkm_input GCA_947484175.1_TH-Jun18-130_genomic.fna/checkm_result
[2023-06-13 15:14:02,566] [INFO] Task succeeded: CheckM
[2023-06-13 15:14:02,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:14:02,600] [INFO] ===== Completeness check finished =====
[2023-06-13 15:14:02,601] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:14:02,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947484175.1_TH-Jun18-130_genomic.fna/markers.fasta)
[2023-06-13 15:14:02,601] [INFO] Task started: Blastn
[2023-06-13 15:14:02,601] [INFO] Running command: blastn -query GCA_947484175.1_TH-Jun18-130_genomic.fna/markers.fasta -db /var/lib/cwl/stg84ed0cd3-39b4-41d4-969b-483e9384c9e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_947484175.1_TH-Jun18-130_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:14:03,514] [INFO] Task succeeded: Blastn
[2023-06-13 15:14:03,518] [INFO] Selected 14 target genomes.
[2023-06-13 15:14:03,519] [INFO] Target genome list was writen to GCA_947484175.1_TH-Jun18-130_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:14:03,550] [INFO] Task started: fastANI
[2023-06-13 15:14:03,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da79bea-881e-44ea-8a0f-08b080c24f77/GCA_947484175.1_TH-Jun18-130_genomic.fna.gz --refList GCA_947484175.1_TH-Jun18-130_genomic.fna/target_genomes_gtdb.txt --output GCA_947484175.1_TH-Jun18-130_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:14:15,143] [INFO] Task succeeded: fastANI
[2023-06-13 15:14:15,159] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:14:15,159] [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
GCA_903885375.1	s__SXON01 sp903885375	80.5801	964	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.89	0.96	0.95	10	-
GCA_903921785.1	s__SXON01 sp903921785	77.7463	555	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_005776735.1	s__SXON01 sp005776735	77.635	449	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	77.6167	389	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875435.1	s__SXON01 sp016875435	77.4179	405	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692585.1	s__SXON01 sp009692585	77.3515	389	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014191855.1	s__SXON01 sp014191855	77.2101	456	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900265.1	s__CAIUMM01 sp903900265	76.1721	190	1370	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	98.89	95.85	0.93	0.87	5	-
GCF_900112685.1	s__Roseivivax sediminis	74.7542	55	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:14:15,161] [INFO] GTDB search result was written to GCA_947484175.1_TH-Jun18-130_genomic.fna/result_gtdb.tsv
[2023-06-13 15:14:15,162] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:14:15,166] [INFO] DFAST_QC result json was written to GCA_947484175.1_TH-Jun18-130_genomic.fna/dqc_result.json
[2023-06-13 15:14:15,166] [INFO] DFAST_QC completed!
[2023-06-13 15:14:15,166] [INFO] Total running time: 0h1m41s