[2024-01-25 18:48:20,400] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:20,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:20,402] [INFO] DQC Reference Directory: /var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference
[2024-01-25 18:48:21,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:21,517] [INFO] Task started: Prodigal
[2024-01-25 18:48:21,517] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8e77802-7566-4471-82d0-94d975031b50/GCF_002285415.1_ASM228541v1_genomic.fna.gz | prodigal -d GCF_002285415.1_ASM228541v1_genomic.fna/cds.fna -a GCF_002285415.1_ASM228541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:31,643] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:31,644] [INFO] Task started: HMMsearch
[2024-01-25 18:48:31,644] [INFO] Running command: hmmsearch --tblout GCF_002285415.1_ASM228541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference/reference_markers.hmm GCF_002285415.1_ASM228541v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:31,842] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:31,843] [INFO] Found 6/6 markers.
[2024-01-25 18:48:31,869] [INFO] Query marker FASTA was written to GCF_002285415.1_ASM228541v1_genomic.fna/markers.fasta
[2024-01-25 18:48:31,870] [INFO] Task started: Blastn
[2024-01-25 18:48:31,870] [INFO] Running command: blastn -query GCF_002285415.1_ASM228541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference/reference_markers.fasta -out GCF_002285415.1_ASM228541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:32,685] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:32,688] [INFO] Selected 24 target genomes.
[2024-01-25 18:48:32,688] [INFO] Target genome list was writen to GCF_002285415.1_ASM228541v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:32,702] [INFO] Task started: fastANI
[2024-01-25 18:48:32,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e77802-7566-4471-82d0-94d975031b50/GCF_002285415.1_ASM228541v1_genomic.fna.gz --refList GCF_002285415.1_ASM228541v1_genomic.fna/target_genomes.txt --output GCF_002285415.1_ASM228541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:49,692] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:49,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:49,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:49,706] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:48:49,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:49,707] [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
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	100.0	1160	1162	95	conclusive
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	99.9992	1151	1162	95	conclusive
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.6413	314	1162	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.1428	283	1162	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.0583	250	1162	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	77.9871	306	1162	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.9499	257	1162	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.8403	259	1162	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.8318	260	1162	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.733	250	1162	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	77.6853	229	1162	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.6562	186	1162	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	77.6477	248	1162	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	77.5918	225	1162	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5841	187	1162	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.5766	265	1162	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	77.36	175	1162	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	77.3313	214	1162	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.2945	216	1162	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2521	232	1162	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.2253	219	1162	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.2111	229	1162	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.1602	196	1162	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.1075	227	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:49,708] [INFO] DFAST Taxonomy check result was written to GCF_002285415.1_ASM228541v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:49,708] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:49,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:49,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference/checkm_data
[2024-01-25 18:48:49,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:49,747] [INFO] Task started: CheckM
[2024-01-25 18:48:49,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002285415.1_ASM228541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002285415.1_ASM228541v1_genomic.fna/checkm_input GCF_002285415.1_ASM228541v1_genomic.fna/checkm_result
[2024-01-25 18:49:22,411] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:22,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:22,431] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:22,432] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:22,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002285415.1_ASM228541v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:22,432] [INFO] Task started: Blastn
[2024-01-25 18:49:22,432] [INFO] Running command: blastn -query GCF_002285415.1_ASM228541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda22cd0d-4132-4513-a984-2f610d55e19e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002285415.1_ASM228541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:23,964] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:23,968] [INFO] Selected 23 target genomes.
[2024-01-25 18:49:23,968] [INFO] Target genome list was writen to GCF_002285415.1_ASM228541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:23,988] [INFO] Task started: fastANI
[2024-01-25 18:49:23,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e77802-7566-4471-82d0-94d975031b50/GCF_002285415.1_ASM228541v1_genomic.fna.gz --refList GCF_002285415.1_ASM228541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002285415.1_ASM228541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:42,974] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:42,987] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:42,987] [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_002285415.1	s__Actibacterium pelagium	100.0	1158	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002285435.1	s__Actibacterium ureilyticum	78.7017	402	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000671395.1	s__Actibacterium atlanticum	78.6273	314	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	78.4901	320	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	78.4322	380	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706605.1	s__SAT37 sp002706605	78.2918	312	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCF_000813965.1	s__Leisingera sp000813965	78.0532	251	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	78.0363	292	1162	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_014196965.1	s__Actibacterium_A naphthalenivorans	78.0213	307	1162	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_018139985.1	s__JAGSOU01 sp018139985	77.9512	326	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	77.9496	265	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	77.9176	259	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	77.9065	290	1162	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_000813725.1	s__Leisingera sp000813725	77.8715	272	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	77.7723	262	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.7708	258	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	77.7342	283	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	77.6427	187	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	77.5291	282	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_017744095.1	s__Shimia sp017744095	77.5017	209	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	77.4377	286	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	77.2313	219	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107015.1	s__Litoreibacter albidus	77.2115	173	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:42,988] [INFO] GTDB search result was written to GCF_002285415.1_ASM228541v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:42,989] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:42,992] [INFO] DFAST_QC result json was written to GCF_002285415.1_ASM228541v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:42,993] [INFO] DFAST_QC completed!
[2024-01-25 18:49:42,993] [INFO] Total running time: 0h1m23s