[2024-01-25 18:14:05,812] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,815] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference
[2024-01-25 18:14:06,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,951] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d41c50c-fdd4-4811-b912-7b32fa16cd56/GCF_014637625.1_ASM1463762v1_genomic.fna.gz | prodigal -d GCF_014637625.1_ASM1463762v1_genomic.fna/cds.fna -a GCF_014637625.1_ASM1463762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:15,157] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:15,157] [INFO] Task started: HMMsearch
[2024-01-25 18:14:15,157] [INFO] Running command: hmmsearch --tblout GCF_014637625.1_ASM1463762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference/reference_markers.hmm GCF_014637625.1_ASM1463762v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:15,367] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:15,368] [INFO] Found 6/6 markers.
[2024-01-25 18:14:15,393] [INFO] Query marker FASTA was written to GCF_014637625.1_ASM1463762v1_genomic.fna/markers.fasta
[2024-01-25 18:14:15,393] [INFO] Task started: Blastn
[2024-01-25 18:14:15,393] [INFO] Running command: blastn -query GCF_014637625.1_ASM1463762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference/reference_markers.fasta -out GCF_014637625.1_ASM1463762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:16,211] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:16,214] [INFO] Selected 16 target genomes.
[2024-01-25 18:14:16,214] [INFO] Target genome list was writen to GCF_014637625.1_ASM1463762v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:16,225] [INFO] Task started: fastANI
[2024-01-25 18:14:16,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d41c50c-fdd4-4811-b912-7b32fa16cd56/GCF_014637625.1_ASM1463762v1_genomic.fna.gz --refList GCF_014637625.1_ASM1463762v1_genomic.fna/target_genomes.txt --output GCF_014637625.1_ASM1463762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:28,398] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:28,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:28,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:28,410] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:14:28,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:28,410] [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
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	100.0	1010	1010	95	conclusive
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	99.9979	997	1010	95	conclusive
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	86.3387	801	1010	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	78.1727	284	1010	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	78.1306	285	1010	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	78.1216	339	1010	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	78.0914	346	1010	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.6923	292	1010	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.3214	124	1010	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	76.1689	124	1010	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.1683	88	1010	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	76.0768	131	1010	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	76.0584	125	1010	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.0054	98	1010	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	75.9139	102	1010	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.868	65	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:28,412] [INFO] DFAST Taxonomy check result was written to GCF_014637625.1_ASM1463762v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:28,413] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:28,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:28,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference/checkm_data
[2024-01-25 18:14:28,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:28,445] [INFO] Task started: CheckM
[2024-01-25 18:14:28,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637625.1_ASM1463762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637625.1_ASM1463762v1_genomic.fna/checkm_input GCF_014637625.1_ASM1463762v1_genomic.fna/checkm_result
[2024-01-25 18:14:55,365] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:55,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:55,385] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:55,385] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:55,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637625.1_ASM1463762v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:55,386] [INFO] Task started: Blastn
[2024-01-25 18:14:55,386] [INFO] Running command: blastn -query GCF_014637625.1_ASM1463762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0d00e8-20c7-414e-a282-bef5ce07820f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637625.1_ASM1463762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:57,036] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:57,039] [INFO] Selected 13 target genomes.
[2024-01-25 18:14:57,039] [INFO] Target genome list was writen to GCF_014637625.1_ASM1463762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:57,059] [INFO] Task started: fastANI
[2024-01-25 18:14:57,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d41c50c-fdd4-4811-b912-7b32fa16cd56/GCF_014637625.1_ASM1463762v1_genomic.fna.gz --refList GCF_014637625.1_ASM1463762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637625.1_ASM1463762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:05,936] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:05,946] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:05,946] [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_004000605.1	s__Glycocaulis alkaliphilus	99.9979	997	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014639075.1	s__Glycocaulis albus	86.3387	801	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744995.1	s__Glycocaulis sp000744995	82.8873	724	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	98.48	98.48	0.95	0.95	2	-
GCF_000152745.1	s__Oceanicaulis sp000152745	79.0245	318	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_007050995.1	s__Glycocaulis profundi	78.5416	422	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	78.418	409	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.2858	363	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	78.1465	286	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017161425.1	s__Marinicauda algicola	78.0914	346	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003046365.1	s__Oceanicaulis sp003046365	77.7871	250	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCA_001657295.1	s__Oceanicaulis sp001657295	77.1699	263	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008711135.1	s__LNNU-3342 sp008711135	76.3485	51	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LNNU-3342	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977555.1	s__Caulobacter rhizosphaerae	76.1516	125	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.18	95.88	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:05,949] [INFO] GTDB search result was written to GCF_014637625.1_ASM1463762v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:05,950] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:05,954] [INFO] DFAST_QC result json was written to GCF_014637625.1_ASM1463762v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:05,954] [INFO] DFAST_QC completed!
[2024-01-25 18:15:05,954] [INFO] Total running time: 0h1m0s