[2024-01-24 13:31:35,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference
[2024-01-24 13:31:36,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,830] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg85919d50-98a2-43b1-814a-85056c833742/GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/cds.fna -a GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:57,607] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:57,608] [INFO] Task started: HMMsearch
[2024-01-24 13:31:57,608] [INFO] Running command: hmmsearch --tblout GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference/reference_markers.hmm GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:58,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:58,090] [INFO] Found 6/6 markers.
[2024-01-24 13:31:58,148] [INFO] Query marker FASTA was written to GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:31:58,149] [INFO] Task started: Blastn
[2024-01-24 13:31:58,149] [INFO] Running command: blastn -query GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference/reference_markers.fasta -out GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:59,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:59,045] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:59,045] [INFO] Target genome list was writen to GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:31:59,053] [INFO] Task started: fastANI
[2024-01-24 13:31:59,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg85919d50-98a2-43b1-814a-85056c833742/GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna.gz --refList GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:16,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:16,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:16,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:16,592] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:16,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:16,592] [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
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	80.9446	1181	2242	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	80.924	1045	2242	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	80.5292	972	2242	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	78.3484	766	2242	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.661	399	2242	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.6607	253	2242	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.6338	386	2242	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.5677	250	2242	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.5321	331	2242	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.4284	200	2242	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.3692	259	2242	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.3295	288	2242	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.2771	273	2242	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.2519	234	2242	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.1548	276	2242	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.9696	218	2242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,594] [INFO] DFAST Taxonomy check result was written to GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:16,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:16,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:16,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference/checkm_data
[2024-01-24 13:32:16,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:16,664] [INFO] Task started: CheckM
[2024-01-24 13:32:16,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/checkm_input GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:33:16,923] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:16,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,947] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:16,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:16,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:33:16,948] [INFO] Task started: Blastn
[2024-01-24 13:33:16,948] [INFO] Running command: blastn -query GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg67f756b2-cc60-41d9-8060-9e75c3a58081/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:18,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:18,739] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:18,739] [INFO] Target genome list was writen to GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:18,820] [INFO] Task started: fastANI
[2024-01-24 13:33:18,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg85919d50-98a2-43b1-814a-85056c833742/GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna.gz --refList GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:38,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:38,343] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:38,343] [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_900167455.1	s__Reyranella aerosaccus	100.0	2238	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240685.1	s__Reyranella sp018240685	84.7749	1299	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242505.1	s__Reyranella sp018242505	81.4862	1084	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305915.1	s__Reyranella sp017305915	81.3901	1205	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	81.3308	708	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772935.1	s__Reyranella sp009772935	81.284	1032	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308235.1	s__Reyranella sp017308235	81.1629	1103	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240695.1	s__Reyranella sp018240695	81.1157	875	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCA_001897995.1	s__Reyranella sp001897995	81.1115	984	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.19	98.73	0.86	0.86	3	-
GCA_004296815.1	s__Reyranella sp004296815	80.9677	760	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	80.8595	1073	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990895.1	s__Reyranella sp017990895	80.7841	779	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312425.1	s__Reyranella massiliensis	80.5063	975	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205335.1	s__Reyranella sp013205335	80.2383	739	2242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:38,345] [INFO] GTDB search result was written to GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:38,345] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:38,349] [INFO] DFAST_QC result json was written to GCF_900167455.1_IMG-taxon_2582581318_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:33:38,349] [INFO] DFAST_QC completed!
[2024-01-24 13:33:38,349] [INFO] Total running time: 0h2m3s