[2024-01-25 18:14:20,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:20,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:20,529] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference
[2024-01-25 18:14:21,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:21,643] [INFO] Task started: Prodigal
[2024-01-25 18:14:21,643] [INFO] Running command: gunzip -c /var/lib/cwl/stga082cbc9-d6d6-47cb-a134-37420e1c834b/GCF_014640095.1_ASM1464009v1_genomic.fna.gz | prodigal -d GCF_014640095.1_ASM1464009v1_genomic.fna/cds.fna -a GCF_014640095.1_ASM1464009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:30,122] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:30,123] [INFO] Task started: HMMsearch
[2024-01-25 18:14:30,123] [INFO] Running command: hmmsearch --tblout GCF_014640095.1_ASM1464009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference/reference_markers.hmm GCF_014640095.1_ASM1464009v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:30,328] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:30,329] [INFO] Found 6/6 markers.
[2024-01-25 18:14:30,356] [INFO] Query marker FASTA was written to GCF_014640095.1_ASM1464009v1_genomic.fna/markers.fasta
[2024-01-25 18:14:30,356] [INFO] Task started: Blastn
[2024-01-25 18:14:30,357] [INFO] Running command: blastn -query GCF_014640095.1_ASM1464009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference/reference_markers.fasta -out GCF_014640095.1_ASM1464009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:31,230] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:31,233] [INFO] Selected 9 target genomes.
[2024-01-25 18:14:31,233] [INFO] Target genome list was writen to GCF_014640095.1_ASM1464009v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:31,236] [INFO] Task started: fastANI
[2024-01-25 18:14:31,237] [INFO] Running command: fastANI --query /var/lib/cwl/stga082cbc9-d6d6-47cb-a134-37420e1c834b/GCF_014640095.1_ASM1464009v1_genomic.fna.gz --refList GCF_014640095.1_ASM1464009v1_genomic.fna/target_genomes.txt --output GCF_014640095.1_ASM1464009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:38,326] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:38,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:38,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:38,333] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:14:38,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:38,334] [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
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	100.0	1088	1089	95	conclusive
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	99.9984	1044	1089	95	conclusive
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	99.9975	1087	1089	95	conclusive
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	85.9054	895	1089	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	85.8565	909	1089	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.8921	140	1089	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.1617	101	1089	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1006	93	1089	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.8223	125	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:38,335] [INFO] DFAST Taxonomy check result was written to GCF_014640095.1_ASM1464009v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:38,335] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:38,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:38,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference/checkm_data
[2024-01-25 18:14:38,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:38,370] [INFO] Task started: CheckM
[2024-01-25 18:14:38,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640095.1_ASM1464009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640095.1_ASM1464009v1_genomic.fna/checkm_input GCF_014640095.1_ASM1464009v1_genomic.fna/checkm_result
[2024-01-25 18:15:06,222] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:06,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:06,242] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:06,242] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:06,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640095.1_ASM1464009v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:06,243] [INFO] Task started: Blastn
[2024-01-25 18:15:06,243] [INFO] Running command: blastn -query GCF_014640095.1_ASM1464009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4ec46b-fd3b-44c6-9a1b-16d9d4bda3e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640095.1_ASM1464009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:07,990] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:07,993] [INFO] Selected 16 target genomes.
[2024-01-25 18:15:07,993] [INFO] Target genome list was writen to GCF_014640095.1_ASM1464009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:08,006] [INFO] Task started: fastANI
[2024-01-25 18:15:08,006] [INFO] Running command: fastANI --query /var/lib/cwl/stga082cbc9-d6d6-47cb-a134-37420e1c834b/GCF_014640095.1_ASM1464009v1_genomic.fna.gz --refList GCF_014640095.1_ASM1464009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640095.1_ASM1464009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:19,465] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:19,475] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:19,475] [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_014640095.1	s__Aquisalinus flavus	100.0	1088	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009712425.2	s__Aquisalinus luteolus	85.9101	895	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	77.4166	174	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000733125.1	s__Parvularcula oceani	77.3967	268	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943565.1	s__Marinicaulis flavus	77.2596	207	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	77.215	199	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	77.191	171	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085255.1	s__Parvularcula mediterranea	77.134	141	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426945.1	s__Pseudolabrys sp001426945	77.1234	103	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399445.1	s__Parvularcula sp003399445	77.0182	181	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869065.1	s__Rhodobium sp002869065	76.6894	136	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	76.6083	179	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	76.4149	152	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	76.359	132	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241335.1	s__Palsa-881 sp018241335	76.2127	112	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259195.1	s__Paracoccus sediminilitoris	76.1907	78	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:19,477] [INFO] GTDB search result was written to GCF_014640095.1_ASM1464009v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:19,477] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:19,480] [INFO] DFAST_QC result json was written to GCF_014640095.1_ASM1464009v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:19,481] [INFO] DFAST_QC completed!
[2024-01-25 18:15:19,481] [INFO] Total running time: 0h0m59s