[2024-01-24 13:48:58,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:58,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:58,063] [INFO] DQC Reference Directory: /var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference
[2024-01-24 13:48:59,331] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:59,332] [INFO] Task started: Prodigal
[2024-01-24 13:48:59,333] [INFO] Running command: gunzip -c /var/lib/cwl/stg50628154-b278-4bcd-9854-1abc3792f07b/GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/cds.fna -a GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:10,009] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:10,009] [INFO] Task started: HMMsearch
[2024-01-24 13:49:10,010] [INFO] Running command: hmmsearch --tblout GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference/reference_markers.hmm GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:10,266] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:10,268] [INFO] Found 6/6 markers.
[2024-01-24 13:49:10,301] [INFO] Query marker FASTA was written to GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:49:10,302] [INFO] Task started: Blastn
[2024-01-24 13:49:10,302] [INFO] Running command: blastn -query GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference/reference_markers.fasta -out GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:11,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:11,120] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:11,121] [INFO] Target genome list was writen to GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:49:11,129] [INFO] Task started: fastANI
[2024-01-24 13:49:11,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg50628154-b278-4bcd-9854-1abc3792f07b/GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna.gz --refList GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:23,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:23,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:23,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:23,181] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:23,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:23,182] [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
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	100.0	1108	1108	95	conclusive
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	86.2836	872	1108	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	83.9117	762	1108	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	79.8757	543	1108	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	79.3641	413	1108	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	79.3501	521	1108	95	below_threshold
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	79.2671	422	1108	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	77.8356	244	1108	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	77.6072	207	1108	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.5404	242	1108	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.4947	229	1108	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	77.4795	201	1108	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.3452	146	1108	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.291	156	1108	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.1023	172	1108	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.9192	226	1108	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.8795	198	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:23,183] [INFO] DFAST Taxonomy check result was written to GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:49:23,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:23,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:23,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference/checkm_data
[2024-01-24 13:49:23,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:23,222] [INFO] Task started: CheckM
[2024-01-24 13:49:23,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/checkm_input GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:50:01,343] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:01,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,363] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:01,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:01,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:50:01,364] [INFO] Task started: Blastn
[2024-01-24 13:50:01,364] [INFO] Running command: blastn -query GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgba04fed7-4cb2-4660-82df-458e59acaa3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:02,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:02,682] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:02,682] [INFO] Target genome list was writen to GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:02,689] [INFO] Task started: fastANI
[2024-01-24 13:50:02,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg50628154-b278-4bcd-9854-1abc3792f07b/GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna.gz --refList GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:10,077] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:10,086] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:10,087] [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_900302485.1	s__Aliiroseovarius pelagivivens	100.0	1108	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010500215.1	s__Aliiroseovarius sp010500215	86.5571	895	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	86.2836	872	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004645.1	s__Aliiroseovarius halocynthiae	83.9117	762	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656375.1	s__Aliiroseovarius zhejiangensis	79.8857	542	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307765.1	s__Aliiroseovarius crassostreae	79.3641	413	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	-
GCF_900109955.1	s__Aliiroseovarius sediminilitoris	79.3511	522	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367285.1	s__Aliiroseovarius sp002367285	78.0018	309	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550095.1	s__Celeribacter ethanolicus	77.5139	200	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900116005.1	s__Poseidonocella sedimentorum	76.928	159	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:10,088] [INFO] GTDB search result was written to GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:10,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:10,092] [INFO] DFAST_QC result json was written to GCF_900302485.1_A.pelagivivensCECT8811_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:50:10,092] [INFO] DFAST_QC completed!
[2024-01-24 13:50:10,093] [INFO] Total running time: 0h1m12s