[2024-01-24 12:00:36,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference
[2024-01-24 12:00:39,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,379] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,379] [INFO] Running command: gunzip -c /var/lib/cwl/stg41cb4f35-a036-44c1-8bb7-47646d015184/GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/cds.fna -a GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:59,763] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:59,764] [INFO] Task started: HMMsearch
[2024-01-24 12:00:59,764] [INFO] Running command: hmmsearch --tblout GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference/reference_markers.hmm GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:01:00,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:01:00,038] [INFO] Found 6/6 markers.
[2024-01-24 12:01:00,073] [INFO] Query marker FASTA was written to GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 12:01:00,073] [INFO] Task started: Blastn
[2024-01-24 12:01:00,074] [INFO] Running command: blastn -query GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference/reference_markers.fasta -out GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:00,693] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:00,699] [INFO] Selected 12 target genomes.
[2024-01-24 12:01:00,699] [INFO] Target genome list was writen to GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 12:01:00,705] [INFO] Task started: fastANI
[2024-01-24 12:01:00,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg41cb4f35-a036-44c1-8bb7-47646d015184/GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna.gz --refList GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:09,749] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:09,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:09,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:09,763] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:01:09,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:09,763] [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
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	100.0	1408	1408	95	conclusive
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	79.2957	656	1408	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	79.2322	679	1408	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	78.6791	575	1408	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	78.6617	623	1408	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	78.0324	499	1408	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.9317	265	1408	95	below_threshold
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	75.2937	78	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:09,765] [INFO] DFAST Taxonomy check result was written to GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 12:01:09,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:09,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:09,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference/checkm_data
[2024-01-24 12:01:09,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:09,810] [INFO] Task started: CheckM
[2024-01-24 12:01:09,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/checkm_input GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 12:02:05,957] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:05,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:05,981] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:05,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:05,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 12:02:05,982] [INFO] Task started: Blastn
[2024-01-24 12:02:05,982] [INFO] Running command: blastn -query GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgb459e7a2-b999-4ed3-ab99-c65b99e4d432/dqc_reference/reference_markers_gtdb.fasta -out GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:06,855] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:06,860] [INFO] Selected 10 target genomes.
[2024-01-24 12:02:06,860] [INFO] Target genome list was writen to GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:06,869] [INFO] Task started: fastANI
[2024-01-24 12:02:06,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg41cb4f35-a036-44c1-8bb7-47646d015184/GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna.gz --refList GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:15,812] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:15,824] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:02:15,824] [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_002631205.1	s__Lewinella_A marina	79.3032	655	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003390915.1	s__Lewinella_A sp003390915	79.1201	622	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197245.1	s__Lewinella_A aquimaris	78.6683	622	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803465.1	s__Lewinella_A litorea	78.6648	577	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390935.1	s__Lewinella_A sp003390935	78.0831	501	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934605.1	s__Lewinella_A xylanilytica	78.0324	499	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	76.9404	264	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004375085.3	s__Lewinella_A sp004375085	76.6715	252	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:15,826] [INFO] GTDB search result was written to GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:15,826] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:15,830] [INFO] DFAST_QC result json was written to GCF_923081025.1_Lewinella_maritima_CECT_8419_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 12:02:15,830] [INFO] DFAST_QC completed!
[2024-01-24 12:02:15,830] [INFO] Total running time: 0h1m39s