[2023-06-29 06:10:59,477] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:10:59,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:10:59,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference
[2023-06-29 06:11:00,924] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:11:00,926] [INFO] Task started: Prodigal
[2023-06-29 06:11:00,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg87b727ff-439e-466a-bfe1-61e71d7c091d/GCA_020832735.1_ASM2083273v1_genomic.fna.gz | prodigal -d GCA_020832735.1_ASM2083273v1_genomic.fna/cds.fna -a GCA_020832735.1_ASM2083273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:11:08,754] [INFO] Task succeeded: Prodigal
[2023-06-29 06:11:08,755] [INFO] Task started: HMMsearch
[2023-06-29 06:11:08,756] [INFO] Running command: hmmsearch --tblout GCA_020832735.1_ASM2083273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference/reference_markers.hmm GCA_020832735.1_ASM2083273v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:11:09,077] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:11:09,079] [INFO] Found 6/6 markers.
[2023-06-29 06:11:09,122] [INFO] Query marker FASTA was written to GCA_020832735.1_ASM2083273v1_genomic.fna/markers.fasta
[2023-06-29 06:11:09,123] [INFO] Task started: Blastn
[2023-06-29 06:11:09,123] [INFO] Running command: blastn -query GCA_020832735.1_ASM2083273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference/reference_markers.fasta -out GCA_020832735.1_ASM2083273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:11:10,264] [INFO] Task succeeded: Blastn
[2023-06-29 06:11:10,268] [INFO] Selected 24 target genomes.
[2023-06-29 06:11:10,268] [INFO] Target genome list was writen to GCA_020832735.1_ASM2083273v1_genomic.fna/target_genomes.txt
[2023-06-29 06:11:10,275] [INFO] Task started: fastANI
[2023-06-29 06:11:10,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b727ff-439e-466a-bfe1-61e71d7c091d/GCA_020832735.1_ASM2083273v1_genomic.fna.gz --refList GCA_020832735.1_ASM2083273v1_genomic.fna/target_genomes.txt --output GCA_020832735.1_ASM2083273v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:11:28,625] [INFO] Task succeeded: fastANI
[2023-06-29 06:11:28,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:11:28,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:11:28,644] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:11:28,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:11:28,645] [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
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	78.6635	397	847	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	78.5972	378	847	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	78.5215	408	847	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	78.4424	332	847	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	78.2468	353	847	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	78.206	356	847	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	78.1513	304	847	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	78.1312	306	847	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	78.1258	306	847	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	76.8077	132	847	95	below_threshold
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	76.7823	205	847	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	76.757	175	847	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	76.6197	160	847	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	76.5299	111	847	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	76.4028	131	847	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	76.2127	125	847	95	below_threshold
Methylobacterium brachythecii	strain=DSM 24105	GCA_014196345.1	1176177	1176177	type	True	76.1505	89	847	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.1124	140	847	95	below_threshold
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	75.8996	80	847	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	75.8493	80	847	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.6613	130	847	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.651	90	847	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.5914	140	847	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.4981	125	847	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:11:28,652] [INFO] DFAST Taxonomy check result was written to GCA_020832735.1_ASM2083273v1_genomic.fna/tc_result.tsv
[2023-06-29 06:11:28,653] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:11:28,653] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:11:28,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference/checkm_data
[2023-06-29 06:11:28,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:11:28,695] [INFO] Task started: CheckM
[2023-06-29 06:11:28,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020832735.1_ASM2083273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020832735.1_ASM2083273v1_genomic.fna/checkm_input GCA_020832735.1_ASM2083273v1_genomic.fna/checkm_result
[2023-06-29 06:11:58,071] [INFO] Task succeeded: CheckM
[2023-06-29 06:11:58,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:11:58,094] [INFO] ===== Completeness check finished =====
[2023-06-29 06:11:58,094] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:11:58,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020832735.1_ASM2083273v1_genomic.fna/markers.fasta)
[2023-06-29 06:11:58,095] [INFO] Task started: Blastn
[2023-06-29 06:11:58,095] [INFO] Running command: blastn -query GCA_020832735.1_ASM2083273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fb6808a-8889-4791-95b7-d35e80912a97/dqc_reference/reference_markers_gtdb.fasta -out GCA_020832735.1_ASM2083273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:11:59,639] [INFO] Task succeeded: Blastn
[2023-06-29 06:11:59,642] [INFO] Selected 12 target genomes.
[2023-06-29 06:11:59,642] [INFO] Target genome list was writen to GCA_020832735.1_ASM2083273v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:11:59,649] [INFO] Task started: fastANI
[2023-06-29 06:11:59,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b727ff-439e-466a-bfe1-61e71d7c091d/GCA_020832735.1_ASM2083273v1_genomic.fna.gz --refList GCA_020832735.1_ASM2083273v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020832735.1_ASM2083273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:12:07,580] [INFO] Task succeeded: fastANI
[2023-06-29 06:12:07,591] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:12:07,591] [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_008630495.1	s__Oceanicaulis satelles	86.1002	721	847	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	84.5042	673	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050995.1	s__Glycocaulis profundi	79.2533	451	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	78.9243	386	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_017161425.1	s__Marinicauda algicola	78.6217	401	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003122085.1	s__WD6-1 sp003122085	78.6137	377	847	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_000420265.1	s__Oceanicaulis alexandrii	78.4891	373	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCF_014639075.1	s__Glycocaulis albus	78.4555	333	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657295.1	s__Oceanicaulis sp001657295	78.415	376	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046365.1	s__Oceanicaulis sp003046365	78.3382	329	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_004793635.1	s__Marinicauda pacifica	78.1549	304	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002783385.1	s__Hyphobacterium sp002783385	76.5822	105	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:12:07,593] [INFO] GTDB search result was written to GCA_020832735.1_ASM2083273v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:12:07,594] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:12:07,598] [INFO] DFAST_QC result json was written to GCA_020832735.1_ASM2083273v1_genomic.fna/dqc_result.json
[2023-06-29 06:12:07,598] [INFO] DFAST_QC completed!
[2023-06-29 06:12:07,598] [INFO] Total running time: 0h1m8s