[2024-01-24 14:19:18,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference
[2024-01-24 14:19:19,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:19,928] [INFO] Task started: Prodigal
[2024-01-24 14:19:19,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg7726d389-9c86-4cf9-8e43-7bae66a69bba/GCF_000412185.1_jl2009_genomic.fna.gz | prodigal -d GCF_000412185.1_jl2009_genomic.fna/cds.fna -a GCF_000412185.1_jl2009_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:29,368] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:29,368] [INFO] Task started: HMMsearch
[2024-01-24 14:19:29,368] [INFO] Running command: hmmsearch --tblout GCF_000412185.1_jl2009_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference/reference_markers.hmm GCF_000412185.1_jl2009_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:29,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:29,675] [INFO] Found 6/6 markers.
[2024-01-24 14:19:29,706] [INFO] Query marker FASTA was written to GCF_000412185.1_jl2009_genomic.fna/markers.fasta
[2024-01-24 14:19:29,707] [INFO] Task started: Blastn
[2024-01-24 14:19:29,707] [INFO] Running command: blastn -query GCF_000412185.1_jl2009_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference/reference_markers.fasta -out GCF_000412185.1_jl2009_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:30,544] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:30,548] [INFO] Selected 26 target genomes.
[2024-01-24 14:19:30,548] [INFO] Target genome list was writen to GCF_000412185.1_jl2009_genomic.fna/target_genomes.txt
[2024-01-24 14:19:30,566] [INFO] Task started: fastANI
[2024-01-24 14:19:30,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg7726d389-9c86-4cf9-8e43-7bae66a69bba/GCF_000412185.1_jl2009_genomic.fna.gz --refList GCF_000412185.1_jl2009_genomic.fna/target_genomes.txt --output GCF_000412185.1_jl2009_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:48,400] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:48,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:48,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:48,420] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:48,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:48,420] [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
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	100.0	1085	1089	95	conclusive
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.3218	218	1089	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.2474	225	1089	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.2318	229	1089	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.1012	117	1089	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.0419	115	1089	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	77.0315	120	1089	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	76.9689	162	1089	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	76.8128	171	1089	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	76.788	167	1089	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	76.7663	159	1089	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.7193	118	1089	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.6869	115	1089	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.6608	88	1089	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.6206	182	1089	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	76.4544	181	1089	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.4222	138	1089	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.3718	115	1089	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	76.3302	97	1089	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.2972	175	1089	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.254	177	1089	95	below_threshold
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	76.2492	128	1089	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.2425	144	1089	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.1494	164	1089	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.0646	136	1089	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	76.056	92	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:48,422] [INFO] DFAST Taxonomy check result was written to GCF_000412185.1_jl2009_genomic.fna/tc_result.tsv
[2024-01-24 14:19:48,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:48,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:48,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference/checkm_data
[2024-01-24 14:19:48,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:48,462] [INFO] Task started: CheckM
[2024-01-24 14:19:48,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000412185.1_jl2009_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000412185.1_jl2009_genomic.fna/checkm_input GCF_000412185.1_jl2009_genomic.fna/checkm_result
[2024-01-24 14:20:19,042] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:19,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:19,064] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:19,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:19,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000412185.1_jl2009_genomic.fna/markers.fasta)
[2024-01-24 14:20:19,065] [INFO] Task started: Blastn
[2024-01-24 14:20:19,065] [INFO] Running command: blastn -query GCF_000412185.1_jl2009_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ffb429a-c899-4016-ab71-a33134eabf67/dqc_reference/reference_markers_gtdb.fasta -out GCF_000412185.1_jl2009_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:20,531] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:20,540] [INFO] Selected 26 target genomes.
[2024-01-24 14:20:20,540] [INFO] Target genome list was writen to GCF_000412185.1_jl2009_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:20,562] [INFO] Task started: fastANI
[2024-01-24 14:20:20,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg7726d389-9c86-4cf9-8e43-7bae66a69bba/GCF_000412185.1_jl2009_genomic.fna.gz --refList GCF_000412185.1_jl2009_genomic.fna/target_genomes_gtdb.txt --output GCF_000412185.1_jl2009_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:39,084] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:39,103] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:39,104] [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_000412185.1	s__Euryhalocaulis caribicus	100.0	1085	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Euryhalocaulis	95.0	97.11	97.11	0.95	0.95	2	conclusive
GCF_003122085.1	s__WD6-1 sp003122085	77.335	217	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	77.3243	190	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_003046365.1	s__Oceanicaulis sp003046365	77.305	150	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCA_016124205.1	s__Hyphobacterium sp016124205	77.272	159	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161425.1	s__Marinicauda algicola	77.2313	229	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007050995.1	s__Glycocaulis profundi	77.2249	238	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	76.9738	155	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657295.1	s__Oceanicaulis sp001657295	76.9384	174	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349105.1	s__17J80-11 sp014349105	76.9328	174	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466985.1	s__Brevundimonas abyssalis	76.8375	143	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCA_016124675.1	s__Oceanicaulis sp016124675	76.8188	201	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858185.1	s__Caulobacter sp903858185	76.7723	129	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.71	99.71	0.95	0.95	2	-
GCF_004341375.1	s__Rhodothalassium salexigens	76.5254	104	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Rhodothalassium	95.0	97.98	95.92	0.96	0.92	5	-
GCA_018826515.1	s__Brevundimonas sp018826515	76.5084	146	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCF_011045195.1	s__Caulobacter soli	76.4655	180	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	76.4093	172	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCA_903837135.1	s__CAIOYC01 sp903837135	76.3353	149	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.97	99.97	0.97	0.97	3	-
GCF_900148505.1	s__Pseudoxanthobacter soli	76.3101	126	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943565.1	s__Marinicaulis flavus	76.2624	127	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_016892765.1	s__Microvirga sp016892765	76.2503	93	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	76.2425	144	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	76.1925	166	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_903642205.1	s__CAHJWH01 sp903642205	76.1904	114	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAHJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024325.1	s__Roseomonas_A tokyonensis	75.9795	148	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	75.9157	88	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,105] [INFO] GTDB search result was written to GCF_000412185.1_jl2009_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:39,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:39,111] [INFO] DFAST_QC result json was written to GCF_000412185.1_jl2009_genomic.fna/dqc_result.json
[2024-01-24 14:20:39,111] [INFO] DFAST_QC completed!
[2024-01-24 14:20:39,111] [INFO] Total running time: 0h1m20s