[2024-01-24 11:34:40,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference
[2024-01-24 11:34:42,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,375] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,375] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1e43536-2d36-413c-8c4b-f14b36ea057f/GCF_014644355.1_ASM1464435v1_genomic.fna.gz | prodigal -d GCF_014644355.1_ASM1464435v1_genomic.fna/cds.fna -a GCF_014644355.1_ASM1464435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:52,756] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:52,757] [INFO] Task started: HMMsearch
[2024-01-24 11:34:52,757] [INFO] Running command: hmmsearch --tblout GCF_014644355.1_ASM1464435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference/reference_markers.hmm GCF_014644355.1_ASM1464435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,004] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,041] [INFO] Query marker FASTA was written to GCF_014644355.1_ASM1464435v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,042] [INFO] Task started: Blastn
[2024-01-24 11:34:53,042] [INFO] Running command: blastn -query GCF_014644355.1_ASM1464435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference/reference_markers.fasta -out GCF_014644355.1_ASM1464435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:53,898] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:53,901] [INFO] Selected 24 target genomes.
[2024-01-24 11:34:53,901] [INFO] Target genome list was writen to GCF_014644355.1_ASM1464435v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:53,915] [INFO] Task started: fastANI
[2024-01-24 11:34:53,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e43536-2d36-413c-8c4b-f14b36ea057f/GCF_014644355.1_ASM1464435v1_genomic.fna.gz --refList GCF_014644355.1_ASM1464435v1_genomic.fna/target_genomes.txt --output GCF_014644355.1_ASM1464435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:10,293] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:10,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:10,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:10,315] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:10,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:10,315] [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=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	100.0	1152	1152	95	conclusive
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	99.9994	1150	1152	95	conclusive
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.8115	301	1152	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	78.1012	246	1152	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.0856	288	1152	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	78.0722	297	1152	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.0592	243	1152	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.9544	239	1152	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	77.8417	228	1152	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.8289	249	1152	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.6643	251	1152	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.5939	252	1152	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	77.538	215	1152	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.522	195	1152	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	77.4832	215	1152	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.3543	215	1152	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.2831	206	1152	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.2756	213	1152	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.2507	222	1152	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.2492	195	1152	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	77.2475	167	1152	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	77.2427	211	1152	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.1125	213	1152	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.075	193	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:10,317] [INFO] DFAST Taxonomy check result was written to GCF_014644355.1_ASM1464435v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:10,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:10,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:10,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference/checkm_data
[2024-01-24 11:35:10,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:10,362] [INFO] Task started: CheckM
[2024-01-24 11:35:10,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644355.1_ASM1464435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644355.1_ASM1464435v1_genomic.fna/checkm_input GCF_014644355.1_ASM1464435v1_genomic.fna/checkm_result
[2024-01-24 11:35:43,793] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:43,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:43,811] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:43,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:43,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644355.1_ASM1464435v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:43,812] [INFO] Task started: Blastn
[2024-01-24 11:35:43,813] [INFO] Running command: blastn -query GCF_014644355.1_ASM1464435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ee34ae3-a527-4354-8ffc-bab717859b8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644355.1_ASM1464435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:45,320] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:45,324] [INFO] Selected 23 target genomes.
[2024-01-24 11:35:45,324] [INFO] Target genome list was writen to GCF_014644355.1_ASM1464435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:45,340] [INFO] Task started: fastANI
[2024-01-24 11:35:45,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e43536-2d36-413c-8c4b-f14b36ea057f/GCF_014644355.1_ASM1464435v1_genomic.fna.gz --refList GCF_014644355.1_ASM1464435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644355.1_ASM1464435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:01,844] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:01,861] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:01,862] [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	99.9994	1150	1152	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_000671395.1	s__Actibacterium atlanticum	78.8399	299	1152	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	78.7068	309	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	78.6209	384	1152	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	78.6128	294	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCF_000744955.1	s__Actibacterium sp000744955	78.3199	374	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	78.1276	262	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.1034	252	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	78.0813	259	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	77.9741	273	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.9385	326	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	77.9345	257	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.9308	309	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	77.8857	296	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	77.6738	299	1152	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_000153725.1	s__Salipiger bermudensis	77.6054	251	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_017744095.1	s__Shimia sp017744095	77.5902	205	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.519	251	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	77.4713	277	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	77.4156	277	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	77.2756	213	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	77.2623	194	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107015.1	s__Litoreibacter albidus	77.2475	167	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,863] [INFO] GTDB search result was written to GCF_014644355.1_ASM1464435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:01,864] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:01,868] [INFO] DFAST_QC result json was written to GCF_014644355.1_ASM1464435v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:01,868] [INFO] DFAST_QC completed!
[2024-01-24 11:36:01,868] [INFO] Total running time: 0h1m21s