[2024-01-24 13:13:10,367] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:10,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:10,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference
[2024-01-24 13:13:11,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:11,682] [INFO] Task started: Prodigal
[2024-01-24 13:13:11,682] [INFO] Running command: gunzip -c /var/lib/cwl/stgaba6f438-4cfb-425c-b49d-5742dd7acdfb/GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/cds.fna -a GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:22,537] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:22,537] [INFO] Task started: HMMsearch
[2024-01-24 13:13:22,537] [INFO] Running command: hmmsearch --tblout GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference/reference_markers.hmm GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:22,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:22,853] [INFO] Found 6/6 markers.
[2024-01-24 13:13:22,891] [INFO] Query marker FASTA was written to GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:13:22,892] [INFO] Task started: Blastn
[2024-01-24 13:13:22,892] [INFO] Running command: blastn -query GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference/reference_markers.fasta -out GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:23,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:23,832] [INFO] Selected 33 target genomes.
[2024-01-24 13:13:23,832] [INFO] Target genome list was writen to GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:13:24,204] [INFO] Task started: fastANI
[2024-01-24 13:13:24,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba6f438-4cfb-425c-b49d-5742dd7acdfb/GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna.gz --refList GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:49,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:49,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:49,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:49,163] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:49,163] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:49,163] [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
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.5049	522	1200	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.3373	548	1200	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	79.3226	467	1200	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.1533	539	1200	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.1525	549	1200	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.1343	542	1200	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	79.1175	376	1200	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.1163	552	1200	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.9931	501	1200	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.9708	484	1200	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.9329	529	1200	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.9177	432	1200	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	78.8839	430	1200	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.8806	500	1200	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.8594	399	1200	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.8335	397	1200	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.7695	424	1200	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.7554	483	1200	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	78.6821	455	1200	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	78.6447	464	1200	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	78.6255	434	1200	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	78.6056	435	1200	95	below_threshold
Aliiruegeria lutimaris	strain=DSM 25294	GCA_900099935.1	571298	571298	type	True	78.4819	428	1200	95	below_threshold
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	78.4723	444	1200	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.4672	393	1200	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.3971	415	1200	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.382	367	1200	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	78.3552	439	1200	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.323	426	1200	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	78.1637	331	1200	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0421	369	1200	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	77.8113	357	1200	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.5311	214	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:49,165] [INFO] DFAST Taxonomy check result was written to GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:13:49,166] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:49,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:49,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference/checkm_data
[2024-01-24 13:13:49,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:49,206] [INFO] Task started: CheckM
[2024-01-24 13:13:49,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/checkm_input GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:14:27,435] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:27,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:27,456] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:27,456] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:27,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:14:27,457] [INFO] Task started: Blastn
[2024-01-24 13:14:27,457] [INFO] Running command: blastn -query GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg4161c51b-0af0-422a-b6d9-69796f180a41/dqc_reference/reference_markers_gtdb.fasta -out GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:29,067] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:29,072] [INFO] Selected 24 target genomes.
[2024-01-24 13:14:29,072] [INFO] Target genome list was writen to GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:29,100] [INFO] Task started: fastANI
[2024-01-24 13:14:29,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba6f438-4cfb-425c-b49d-5742dd7acdfb/GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna.gz --refList GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:49,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:49,243] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:49,243] [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_900172235.1	s__Pseudoruegeria aquimaris	100.0	1196	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	79.9651	574	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	79.4524	387	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	79.3733	544	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_002300555.1	s__Salipiger sp002300555	79.3491	398	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	79.245	549	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	79.2235	572	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.1239	551	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640115.1	s__Muriiphilus lacisalsi	79.0874	491	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.0695	542	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.9279	431	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.8956	534	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	78.8848	430	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	78.7875	462	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.76	482	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.7243	509	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	78.5253	476	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004146235.1	s__Tropicimonas sp004146235	78.4481	424	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.4297	526	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_004339675.1	s__Rhodovulum steppense	78.3595	419	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	78.3466	440	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	78.3194	368	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002504165.1	s__Pacificitalea manganoxidans	78.0047	368	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCF_900113955.1	s__Celeribacter neptunius	77.8202	356	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:49,245] [INFO] GTDB search result was written to GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:49,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:49,262] [INFO] DFAST_QC result json was written to GCF_900172235.1_Ps.aquimaris_CECT7680_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:14:49,262] [INFO] DFAST_QC completed!
[2024-01-24 13:14:49,262] [INFO] Total running time: 0h1m39s