[2024-01-25 20:14:50,363] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference
[2024-01-25 20:14:51,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,510] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg2598b019-8137-424a-b2a4-da00668ed872/GCF_014636515.1_ASM1463651v1_genomic.fna.gz | prodigal -d GCF_014636515.1_ASM1463651v1_genomic.fna/cds.fna -a GCF_014636515.1_ASM1463651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:00,200] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:00,201] [INFO] Task started: HMMsearch
[2024-01-25 20:15:00,201] [INFO] Running command: hmmsearch --tblout GCF_014636515.1_ASM1463651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference/reference_markers.hmm GCF_014636515.1_ASM1463651v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:00,420] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:00,421] [INFO] Found 6/6 markers.
[2024-01-25 20:15:00,448] [INFO] Query marker FASTA was written to GCF_014636515.1_ASM1463651v1_genomic.fna/markers.fasta
[2024-01-25 20:15:00,448] [INFO] Task started: Blastn
[2024-01-25 20:15:00,448] [INFO] Running command: blastn -query GCF_014636515.1_ASM1463651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference/reference_markers.fasta -out GCF_014636515.1_ASM1463651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:01,065] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:01,070] [INFO] Selected 10 target genomes.
[2024-01-25 20:15:01,071] [INFO] Target genome list was writen to GCF_014636515.1_ASM1463651v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:01,074] [INFO] Task started: fastANI
[2024-01-25 20:15:01,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg2598b019-8137-424a-b2a4-da00668ed872/GCF_014636515.1_ASM1463651v1_genomic.fna.gz --refList GCF_014636515.1_ASM1463651v1_genomic.fna/target_genomes.txt --output GCF_014636515.1_ASM1463651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:07,808] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:07,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:07,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:07,816] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:15:07,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:07,817] [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 marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	100.0	1072	1073	95	conclusive
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	99.9971	1071	1073	95	conclusive
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	85.4224	681	1073	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	81.8203	586	1073	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	81.5415	573	1073	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.2564	184	1073	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.2015	178	1073	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.1837	182	1073	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.0164	191	1073	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.883	165	1073	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:07,818] [INFO] DFAST Taxonomy check result was written to GCF_014636515.1_ASM1463651v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:07,818] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:07,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:07,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference/checkm_data
[2024-01-25 20:15:07,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:07,855] [INFO] Task started: CheckM
[2024-01-25 20:15:07,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636515.1_ASM1463651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636515.1_ASM1463651v1_genomic.fna/checkm_input GCF_014636515.1_ASM1463651v1_genomic.fna/checkm_result
[2024-01-25 20:15:36,796] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:36,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:36,813] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:36,813] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:36,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636515.1_ASM1463651v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:36,814] [INFO] Task started: Blastn
[2024-01-25 20:15:36,814] [INFO] Running command: blastn -query GCF_014636515.1_ASM1463651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb54221a8-53b1-4e28-89e6-328db02f91fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636515.1_ASM1463651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:37,680] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:37,683] [INFO] Selected 8 target genomes.
[2024-01-25 20:15:37,684] [INFO] Target genome list was writen to GCF_014636515.1_ASM1463651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:37,688] [INFO] Task started: fastANI
[2024-01-25 20:15:37,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg2598b019-8137-424a-b2a4-da00668ed872/GCF_014636515.1_ASM1463651v1_genomic.fna.gz --refList GCF_014636515.1_ASM1463651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636515.1_ASM1463651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:42,982] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:42,988] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:42,988] [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_900130035.1	s__Wenyingzhuangia marina	99.9971	1071	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	85.4197	681	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	81.8173	587	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	81.567	572	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220525.1	s__Ochrovirga pacifica	79.1731	391	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ochrovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	77.3221	134	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.7422	146	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.534	90	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:42,990] [INFO] GTDB search result was written to GCF_014636515.1_ASM1463651v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:42,990] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:42,998] [INFO] DFAST_QC result json was written to GCF_014636515.1_ASM1463651v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:42,998] [INFO] DFAST_QC completed!
[2024-01-25 20:15:42,998] [INFO] Total running time: 0h0m53s