[2024-01-24 14:19:21,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:21,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:21,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference
[2024-01-24 14:19:23,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:23,553] [INFO] Task started: Prodigal
[2024-01-24 14:19:23,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cc6900b-589c-44d1-bcbf-bd8dc6d3862a/GCF_024346915.1_ASM2434691v1_genomic.fna.gz | prodigal -d GCF_024346915.1_ASM2434691v1_genomic.fna/cds.fna -a GCF_024346915.1_ASM2434691v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:41,984] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:41,984] [INFO] Task started: HMMsearch
[2024-01-24 14:19:41,984] [INFO] Running command: hmmsearch --tblout GCF_024346915.1_ASM2434691v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference/reference_markers.hmm GCF_024346915.1_ASM2434691v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:42,481] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:42,483] [INFO] Found 6/6 markers.
[2024-01-24 14:19:42,547] [INFO] Query marker FASTA was written to GCF_024346915.1_ASM2434691v1_genomic.fna/markers.fasta
[2024-01-24 14:19:42,548] [INFO] Task started: Blastn
[2024-01-24 14:19:42,548] [INFO] Running command: blastn -query GCF_024346915.1_ASM2434691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference/reference_markers.fasta -out GCF_024346915.1_ASM2434691v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:44,818] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:44,822] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:44,823] [INFO] Target genome list was writen to GCF_024346915.1_ASM2434691v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:44,843] [INFO] Task started: fastANI
[2024-01-24 14:19:44,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cc6900b-589c-44d1-bcbf-bd8dc6d3862a/GCF_024346915.1_ASM2434691v1_genomic.fna.gz --refList GCF_024346915.1_ASM2434691v1_genomic.fna/target_genomes.txt --output GCF_024346915.1_ASM2434691v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:00,415] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:00,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:00,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:00,464] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:20:00,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:00,464] [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
Vibrio gazogenes	strain=ATCC 29988	GCA_024346915.1	687	687	type	True	100.0	1570	1570	95	conclusive
Vibrio gazogenes	strain=PB1	GCA_023920225.1	687	687	type	True	99.9996	1567	1570	95	conclusive
Vibrio gazogenes	strain=DSM 21264	GCA_900129185.1	687	687	type	True	99.9553	1520	1570	95	conclusive
Vibrio gazogenes	strain=type strain: CECT 5068	GCA_900163915.1	687	687	type	True	99.8928	1226	1570	95	conclusive
Vibrio spartinae	strain=CECT 9026	GCA_900149295.1	1918945	1918945	type	True	91.9175	1317	1570	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	91.8851	1365	1570	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	85.7557	1203	1570	95	below_threshold
Vibrio mangrovi	strain=CECT 7927	GCA_024346955.1	474394	474394	type	True	81.6427	875	1570	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.381	187	1570	95	below_threshold
Vibrio plantisponsor	strain=LMG 24470	GCA_013041605.1	664643	664643	type	True	78.2593	196	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:00,468] [INFO] DFAST Taxonomy check result was written to GCF_024346915.1_ASM2434691v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:00,469] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:00,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:00,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference/checkm_data
[2024-01-24 14:20:00,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:00,529] [INFO] Task started: CheckM
[2024-01-24 14:20:00,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346915.1_ASM2434691v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346915.1_ASM2434691v1_genomic.fna/checkm_input GCF_024346915.1_ASM2434691v1_genomic.fna/checkm_result
[2024-01-24 14:21:04,208] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:04,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:04,233] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:04,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:04,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346915.1_ASM2434691v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:04,234] [INFO] Task started: Blastn
[2024-01-24 14:21:04,234] [INFO] Running command: blastn -query GCF_024346915.1_ASM2434691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcedaa01-f5e8-406d-adc7-48c8a1ceb01d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346915.1_ASM2434691v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:07,142] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:07,147] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:07,148] [INFO] Target genome list was writen to GCF_024346915.1_ASM2434691v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:07,156] [INFO] Task started: fastANI
[2024-01-24 14:21:07,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cc6900b-589c-44d1-bcbf-bd8dc6d3862a/GCF_024346915.1_ASM2434691v1_genomic.fna.gz --refList GCF_024346915.1_ASM2434691v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346915.1_ASM2434691v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:19,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:19,498] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:19,499] [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_900129185.1	s__Vibrio gazogenes	99.9553	1520	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_002196515.1	s__Vibrio gazogenes_A	94.1872	1383	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900149295.1	s__Vibrio spartinae	91.9067	1318	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.28	99.28	0.90	0.90	2	-
GCF_001506075.1	s__Vibrio sp001506075	88.1724	1223	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163965.1	s__Vibrio ruber	86.5346	1201	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711805.1	s__Vibrio rhizosphaerae	85.6397	1172	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064285.1	s__Vibrio ziniensis	78.9545	189	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740015.1	s__Vibrio diazotrophicus	78.365	188	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_013041605.1	s__Vibrio plantisponsor	78.2522	196	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_014596725.1	s__Vibrio sp014596725	78.1578	194	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:19,500] [INFO] GTDB search result was written to GCF_024346915.1_ASM2434691v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:19,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:19,505] [INFO] DFAST_QC result json was written to GCF_024346915.1_ASM2434691v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:19,506] [INFO] DFAST_QC completed!
[2024-01-24 14:21:19,506] [INFO] Total running time: 0h1m58s