[2024-01-24 11:12:28,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference
[2024-01-24 11:12:29,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,507] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,507] [INFO] Running command: gunzip -c /var/lib/cwl/stged2e6f95-a21f-4037-ae2a-337acb59123e/GCF_014643735.1_ASM1464373v1_genomic.fna.gz | prodigal -d GCF_014643735.1_ASM1464373v1_genomic.fna/cds.fna -a GCF_014643735.1_ASM1464373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:43,284] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:43,284] [INFO] Task started: HMMsearch
[2024-01-24 11:12:43,284] [INFO] Running command: hmmsearch --tblout GCF_014643735.1_ASM1464373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference/reference_markers.hmm GCF_014643735.1_ASM1464373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:43,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:43,608] [INFO] Found 6/6 markers.
[2024-01-24 11:12:43,646] [INFO] Query marker FASTA was written to GCF_014643735.1_ASM1464373v1_genomic.fna/markers.fasta
[2024-01-24 11:12:43,646] [INFO] Task started: Blastn
[2024-01-24 11:12:43,646] [INFO] Running command: blastn -query GCF_014643735.1_ASM1464373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference/reference_markers.fasta -out GCF_014643735.1_ASM1464373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:44,324] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:44,328] [INFO] Selected 33 target genomes.
[2024-01-24 11:12:44,328] [INFO] Target genome list was writen to GCF_014643735.1_ASM1464373v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:44,341] [INFO] Task started: fastANI
[2024-01-24 11:12:44,341] [INFO] Running command: fastANI --query /var/lib/cwl/stged2e6f95-a21f-4037-ae2a-337acb59123e/GCF_014643735.1_ASM1464373v1_genomic.fna.gz --refList GCF_014643735.1_ASM1464373v1_genomic.fna/target_genomes.txt --output GCF_014643735.1_ASM1464373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:06,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:06,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:06,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:06,887] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:06,887] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:06,888] [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
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.842	169	1384	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.799	124	1384	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	77.7947	149	1384	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	77.6993	147	1384	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.6388	125	1384	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.4931	127	1384	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.4486	134	1384	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.386	206	1384	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.3795	124	1384	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.2665	166	1384	95	below_threshold
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	77.0387	127	1384	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	77.0351	140	1384	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.0205	152	1384	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	76.8627	133	1384	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	76.8449	152	1384	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.7947	163	1384	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	76.7611	151	1384	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	76.7151	122	1384	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.7088	84	1384	95	below_threshold
Aquimixticola soesokkakensis	strain=CECT 8620	GCA_900172375.1	1519096	1519096	type	True	76.6893	117	1384	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.6888	152	1384	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	76.6882	122	1384	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.5788	159	1384	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	76.5716	160	1384	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	76.3848	119	1384	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	76.3665	170	1384	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.3095	82	1384	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	76.1068	150	1384	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.077	113	1384	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	76.016	97	1384	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	75.8994	78	1384	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	75.8451	80	1384	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	75.6886	82	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:06,890] [INFO] DFAST Taxonomy check result was written to GCF_014643735.1_ASM1464373v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:06,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:06,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:06,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference/checkm_data
[2024-01-24 11:13:06,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:06,934] [INFO] Task started: CheckM
[2024-01-24 11:13:06,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643735.1_ASM1464373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643735.1_ASM1464373v1_genomic.fna/checkm_input GCF_014643735.1_ASM1464373v1_genomic.fna/checkm_result
[2024-01-24 11:13:48,236] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:48,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:48,259] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:48,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:48,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643735.1_ASM1464373v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:48,260] [INFO] Task started: Blastn
[2024-01-24 11:13:48,260] [INFO] Running command: blastn -query GCF_014643735.1_ASM1464373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9380e1b-cc27-45a8-964e-2ca5701ee894/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643735.1_ASM1464373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:49,283] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:49,287] [INFO] Selected 11 target genomes.
[2024-01-24 11:13:49,288] [INFO] Target genome list was writen to GCF_014643735.1_ASM1464373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:49,301] [INFO] Task started: fastANI
[2024-01-24 11:13:49,301] [INFO] Running command: fastANI --query /var/lib/cwl/stged2e6f95-a21f-4037-ae2a-337acb59123e/GCF_014643735.1_ASM1464373v1_genomic.fna.gz --refList GCF_014643735.1_ASM1464373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643735.1_ASM1464373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:59,390] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:59,405] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:59,405] [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_014643735.1	s__Amylibacter cionae	100.0	1384	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001719615.1	s__Amylibacter sediminis	85.9779	1093	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860325.1	s__Amylibacter lutimaris	84.9286	1057	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223125.1	s__Amylibacter sp018223125	84.832	1013	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108225.1	s__Thalassococcus halodurans	77.7789	149	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus	95.0	96.13	96.13	0.95	0.95	2	-
GCA_018607905.1	s__Amylibacter sp002387535	77.671	275	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.84	99.84	0.91	0.91	2	-
GCF_001518015.1	s__Epibacterium horizontis	77.2244	156	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	76.8115	174	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169455.1	s__Pseudophaeobacter sp000169455	76.5014	113	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764475.1	s__Amylibacter sp016764475	76.4087	109	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254295.1	s__Rhodobacter capsulatus	76.0311	96	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:59,407] [INFO] GTDB search result was written to GCF_014643735.1_ASM1464373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:59,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:59,412] [INFO] DFAST_QC result json was written to GCF_014643735.1_ASM1464373v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:59,412] [INFO] DFAST_QC completed!
[2024-01-24 11:13:59,412] [INFO] Total running time: 0h1m31s