[2024-01-25 18:25:20,546] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference
[2024-01-25 18:25:21,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:21,685] [INFO] Task started: Prodigal
[2024-01-25 18:25:21,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg722c5e34-279e-4078-805f-ed8de1ff06dc/GCF_011927765.1_ASM1192776v1_genomic.fna.gz | prodigal -d GCF_011927765.1_ASM1192776v1_genomic.fna/cds.fna -a GCF_011927765.1_ASM1192776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:30,688] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:30,689] [INFO] Task started: HMMsearch
[2024-01-25 18:25:30,689] [INFO] Running command: hmmsearch --tblout GCF_011927765.1_ASM1192776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference/reference_markers.hmm GCF_011927765.1_ASM1192776v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:30,917] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:30,918] [INFO] Found 6/6 markers.
[2024-01-25 18:25:30,946] [INFO] Query marker FASTA was written to GCF_011927765.1_ASM1192776v1_genomic.fna/markers.fasta
[2024-01-25 18:25:30,947] [INFO] Task started: Blastn
[2024-01-25 18:25:30,947] [INFO] Running command: blastn -query GCF_011927765.1_ASM1192776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference/reference_markers.fasta -out GCF_011927765.1_ASM1192776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:31,553] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:31,556] [INFO] Selected 10 target genomes.
[2024-01-25 18:25:31,556] [INFO] Target genome list was writen to GCF_011927765.1_ASM1192776v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:31,568] [INFO] Task started: fastANI
[2024-01-25 18:25:31,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg722c5e34-279e-4078-805f-ed8de1ff06dc/GCF_011927765.1_ASM1192776v1_genomic.fna.gz --refList GCF_011927765.1_ASM1192776v1_genomic.fna/target_genomes.txt --output GCF_011927765.1_ASM1192776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:38,435] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:38,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:38,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:38,443] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:25:38,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:38,444] [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
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	100.0	1156	1156	95	conclusive
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	84.447	837	1156	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	82.2757	634	1156	95	below_threshold
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	82.0278	585	1156	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	81.949	582	1156	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.476	180	1156	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.3926	178	1156	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.388	179	1156	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.958	192	1156	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.9213	183	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:38,445] [INFO] DFAST Taxonomy check result was written to GCF_011927765.1_ASM1192776v1_genomic.fna/tc_result.tsv
[2024-01-25 18:25:38,446] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:38,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:38,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference/checkm_data
[2024-01-25 18:25:38,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:38,485] [INFO] Task started: CheckM
[2024-01-25 18:25:38,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011927765.1_ASM1192776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011927765.1_ASM1192776v1_genomic.fna/checkm_input GCF_011927765.1_ASM1192776v1_genomic.fna/checkm_result
[2024-01-25 18:26:07,895] [INFO] Task succeeded: CheckM
[2024-01-25 18:26:07,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:26:07,952] [INFO] ===== Completeness check finished =====
[2024-01-25 18:26:07,953] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:26:07,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011927765.1_ASM1192776v1_genomic.fna/markers.fasta)
[2024-01-25 18:26:07,954] [INFO] Task started: Blastn
[2024-01-25 18:26:07,954] [INFO] Running command: blastn -query GCF_011927765.1_ASM1192776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f986a35-3cd5-41a0-a4c5-517f954781fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_011927765.1_ASM1192776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:08,818] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:08,822] [INFO] Selected 6 target genomes.
[2024-01-25 18:26:08,822] [INFO] Target genome list was writen to GCF_011927765.1_ASM1192776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:08,834] [INFO] Task started: fastANI
[2024-01-25 18:26:08,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg722c5e34-279e-4078-805f-ed8de1ff06dc/GCF_011927765.1_ASM1192776v1_genomic.fna.gz --refList GCF_011927765.1_ASM1192776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011927765.1_ASM1192776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:13,528] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:13,533] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:13,534] [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_011927765.1	s__Wenyingzhuangia aestuarii	100.0	1156	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011762155.1	s__Wenyingzhuangia heitensis	84.4326	838	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	82.2362	636	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130035.1	s__Wenyingzhuangia marina	82.0085	587	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220525.1	s__Ochrovirga pacifica	78.9454	480	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ochrovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	77.2759	156	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:13,535] [INFO] GTDB search result was written to GCF_011927765.1_ASM1192776v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:13,535] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:13,538] [INFO] DFAST_QC result json was written to GCF_011927765.1_ASM1192776v1_genomic.fna/dqc_result.json
[2024-01-25 18:26:13,538] [INFO] DFAST_QC completed!
[2024-01-25 18:26:13,539] [INFO] Total running time: 0h0m53s