[2024-01-24 12:13:29,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:29,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:29,023] [INFO] DQC Reference Directory: /var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference
[2024-01-24 12:13:30,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,491] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,491] [INFO] Running command: gunzip -c /var/lib/cwl/stg86f27896-6e01-43ce-87a8-870729965806/GCF_003046545.1_ASM304654v1_genomic.fna.gz | prodigal -d GCF_003046545.1_ASM304654v1_genomic.fna/cds.fna -a GCF_003046545.1_ASM304654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:39,631] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:39,631] [INFO] Task started: HMMsearch
[2024-01-24 12:13:39,631] [INFO] Running command: hmmsearch --tblout GCF_003046545.1_ASM304654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference/reference_markers.hmm GCF_003046545.1_ASM304654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:39,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:39,942] [INFO] Found 6/6 markers.
[2024-01-24 12:13:39,989] [INFO] Query marker FASTA was written to GCF_003046545.1_ASM304654v1_genomic.fna/markers.fasta
[2024-01-24 12:13:39,989] [INFO] Task started: Blastn
[2024-01-24 12:13:39,989] [INFO] Running command: blastn -query GCF_003046545.1_ASM304654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference/reference_markers.fasta -out GCF_003046545.1_ASM304654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:40,830] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:40,833] [INFO] Selected 21 target genomes.
[2024-01-24 12:13:40,833] [INFO] Target genome list was writen to GCF_003046545.1_ASM304654v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:40,854] [INFO] Task started: fastANI
[2024-01-24 12:13:40,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg86f27896-6e01-43ce-87a8-870729965806/GCF_003046545.1_ASM304654v1_genomic.fna.gz --refList GCF_003046545.1_ASM304654v1_genomic.fna/target_genomes.txt --output GCF_003046545.1_ASM304654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,270] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:55,287] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:55,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:55,288] [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
Rhodovulum imhoffii	strain=DSM 18064	GCA_003046545.1	365340	365340	type	True	100.0	937	937	95	conclusive
Rhodovulum imhoffii	strain=DSM 18064	GCA_016653305.1	365340	365340	type	True	99.9369	902	937	95	conclusive
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.7313	437	937	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.6643	394	937	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.6423	399	937	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.6158	402	937	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	78.4812	421	937	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3456	377	937	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.1051	360	937	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	77.6548	214	937	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.5747	221	937	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.5605	222	937	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.4877	270	937	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2625	251	937	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	77.2485	225	937	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.2336	228	937	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	77.1231	210	937	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.1129	207	937	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.0155	210	937	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.0051	218	937	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.9453	209	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:55,289] [INFO] DFAST Taxonomy check result was written to GCF_003046545.1_ASM304654v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:55,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:55,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:55,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference/checkm_data
[2024-01-24 12:13:55,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:55,321] [INFO] Task started: CheckM
[2024-01-24 12:13:55,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003046545.1_ASM304654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003046545.1_ASM304654v1_genomic.fna/checkm_input GCF_003046545.1_ASM304654v1_genomic.fna/checkm_result
[2024-01-24 12:14:26,948] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:26,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:26,971] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:26,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:26,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003046545.1_ASM304654v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:26,973] [INFO] Task started: Blastn
[2024-01-24 12:14:26,973] [INFO] Running command: blastn -query GCF_003046545.1_ASM304654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9113c7f-fdf7-4396-92dd-a8b5747df560/dqc_reference/reference_markers_gtdb.fasta -out GCF_003046545.1_ASM304654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:28,444] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:28,448] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:28,448] [INFO] Target genome list was writen to GCF_003046545.1_ASM304654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:28,465] [INFO] Task started: fastANI
[2024-01-24 12:14:28,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg86f27896-6e01-43ce-87a8-870729965806/GCF_003046545.1_ASM304654v1_genomic.fna.gz --refList GCF_003046545.1_ASM304654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003046545.1_ASM304654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:43,059] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:43,083] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:43,083] [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_003046545.1	s__Rhodovulum imhoffii	100.0	937	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCF_003944755.1	s__Rhodovulum robiginosum	78.7314	436	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	78.6601	398	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004343075.1	s__Rhodovulum marinum	78.4812	421	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	78.4683	389	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343505.1	s__Rhodovulum bhavnagarense	78.3494	356	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002079305.1	s__Rhodovulum sp002079305	78.2887	362	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.2013	365	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	78.1529	338	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	78.1153	359	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.9245	346	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_002927635.1	s__Albidovulum inexpectatum	77.6548	214	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	77.54	292	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.4985	269	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	77.4887	267	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	77.4313	266	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	77.2741	201	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.238	225	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013093415.1	s__Halovulum dunhuangense	77.1319	208	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	76.9597	219	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.9576	208	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.5928	119	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:43,089] [INFO] GTDB search result was written to GCF_003046545.1_ASM304654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:43,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:43,094] [INFO] DFAST_QC result json was written to GCF_003046545.1_ASM304654v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:43,095] [INFO] DFAST_QC completed!
[2024-01-24 12:14:43,095] [INFO] Total running time: 0h1m14s