[2024-01-25 19:05:50,428] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:50,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:50,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference
[2024-01-25 19:05:51,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:51,624] [INFO] Task started: Prodigal
[2024-01-25 19:05:51,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg5df75c10-6dad-4d41-850a-cdddaa3e396a/GCF_024346755.1_ASM2434675v1_genomic.fna.gz | prodigal -d GCF_024346755.1_ASM2434675v1_genomic.fna/cds.fna -a GCF_024346755.1_ASM2434675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:05,168] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:05,168] [INFO] Task started: HMMsearch
[2024-01-25 19:06:05,168] [INFO] Running command: hmmsearch --tblout GCF_024346755.1_ASM2434675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference/reference_markers.hmm GCF_024346755.1_ASM2434675v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:05,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:05,488] [INFO] Found 6/6 markers.
[2024-01-25 19:06:05,530] [INFO] Query marker FASTA was written to GCF_024346755.1_ASM2434675v1_genomic.fna/markers.fasta
[2024-01-25 19:06:05,530] [INFO] Task started: Blastn
[2024-01-25 19:06:05,530] [INFO] Running command: blastn -query GCF_024346755.1_ASM2434675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference/reference_markers.fasta -out GCF_024346755.1_ASM2434675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:06,212] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:06,215] [INFO] Selected 13 target genomes.
[2024-01-25 19:06:06,215] [INFO] Target genome list was writen to GCF_024346755.1_ASM2434675v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:06,227] [INFO] Task started: fastANI
[2024-01-25 19:06:06,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg5df75c10-6dad-4d41-850a-cdddaa3e396a/GCF_024346755.1_ASM2434675v1_genomic.fna.gz --refList GCF_024346755.1_ASM2434675v1_genomic.fna/target_genomes.txt --output GCF_024346755.1_ASM2434675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:19,390] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:19,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:19,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:19,400] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:06:19,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:19,400] [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 aerogenes	strain=LMG 19650	GCA_024346755.1	92172	92172	type	True	100.0	1785	1788	95	conclusive
Vibrio aerogenes	strain=CECT 7868	GCA_900130105.1	92172	92172	type	True	99.9734	1700	1788	95	conclusive
Vibrio quintilis	strain=CECT 7734	GCA_024529975.1	1117707	1117707	type	True	83.4791	1346	1788	95	below_threshold
Vibrio quintilis		GCA_900143745.1	1117707	1117707	type	True	83.4197	1293	1788	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.4093	119	1788	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.3905	112	1788	95	below_threshold
Vibrio gazogenes	strain=PB1	GCA_023920225.1	687	687	type	True	78.675	291	1788	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	78.422	307	1788	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	78.3978	298	1788	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.3354	158	1788	95	below_threshold
Vibrio ruber	strain=CECT 7878	GCA_900163965.1	184755	184755	type	True	78.1923	296	1788	95	below_threshold
Vibrio rhizosphaerae	strain=DSM 18581	GCA_000711805.1	398736	398736	type	True	77.9258	297	1788	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_900149295.1	1918945	1918945	type	True	77.8134	288	1788	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:19,401] [INFO] DFAST Taxonomy check result was written to GCF_024346755.1_ASM2434675v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:19,402] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:19,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:19,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference/checkm_data
[2024-01-25 19:06:19,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:19,455] [INFO] Task started: CheckM
[2024-01-25 19:06:19,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346755.1_ASM2434675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346755.1_ASM2434675v1_genomic.fna/checkm_input GCF_024346755.1_ASM2434675v1_genomic.fna/checkm_result
[2024-01-25 19:07:07,914] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:07,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:07,933] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:07,933] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:07,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346755.1_ASM2434675v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:07,934] [INFO] Task started: Blastn
[2024-01-25 19:07:07,934] [INFO] Running command: blastn -query GCF_024346755.1_ASM2434675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3218f6b9-0095-4efa-9ae9-7aded9c7610d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346755.1_ASM2434675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:09,031] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:09,062] [INFO] Selected 15 target genomes.
[2024-01-25 19:07:09,062] [INFO] Target genome list was writen to GCF_024346755.1_ASM2434675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:09,087] [INFO] Task started: fastANI
[2024-01-25 19:07:09,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg5df75c10-6dad-4d41-850a-cdddaa3e396a/GCF_024346755.1_ASM2434675v1_genomic.fna.gz --refList GCF_024346755.1_ASM2434675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346755.1_ASM2434675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:23,644] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:23,653] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:23,654] [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_900130105.1	s__Vibrio aerogenes	99.9734	1700	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900143745.1	s__Vibrio quintilis	83.4415	1292	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547935.1	s__Vibrio tritonius	79.1389	155	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176135.1	s__Vibrio coralliilyticus	78.5331	143	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_011064285.1	s__Vibrio ziniensis	78.5069	157	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002196515.1	s__Vibrio gazogenes_A	78.4414	291	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222685.1	s__Vibrio nigripulchritudo	78.3327	117	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.90	96.77	0.92	0.87	18	-
GCF_001506075.1	s__Vibrio sp001506075	78.2754	290	1788	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	78.2232	295	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129185.1	s__Vibrio gazogenes	78.0248	276	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000711805.1	s__Vibrio rhizosphaerae	77.969	294	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222605.1	s__Vibrio ichthyoenteri	77.891	109	1788	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	77.8165	287	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.28	99.28	0.90	0.90	2	-
GCF_013113835.1	s__Vibrio sp013113835	77.8058	137	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841115.1	s__Photobacterium sp014841115	77.2268	90	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.86	98.86	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:23,656] [INFO] GTDB search result was written to GCF_024346755.1_ASM2434675v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:23,657] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:23,660] [INFO] DFAST_QC result json was written to GCF_024346755.1_ASM2434675v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:23,661] [INFO] DFAST_QC completed!
[2024-01-25 19:07:23,661] [INFO] Total running time: 0h1m33s