[2024-01-25 20:05:05,471] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:05,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:05,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference
[2024-01-25 20:05:06,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:06,619] [INFO] Task started: Prodigal
[2024-01-25 20:05:06,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg4da6556c-1ab8-4679-9a7c-39c1e044ef4a/GCF_024347615.1_ASM2434761v1_genomic.fna.gz | prodigal -d GCF_024347615.1_ASM2434761v1_genomic.fna/cds.fna -a GCF_024347615.1_ASM2434761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:20,976] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:20,977] [INFO] Task started: HMMsearch
[2024-01-25 20:05:20,977] [INFO] Running command: hmmsearch --tblout GCF_024347615.1_ASM2434761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference/reference_markers.hmm GCF_024347615.1_ASM2434761v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:21,353] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:21,354] [INFO] Found 6/6 markers.
[2024-01-25 20:05:21,397] [INFO] Query marker FASTA was written to GCF_024347615.1_ASM2434761v1_genomic.fna/markers.fasta
[2024-01-25 20:05:21,398] [INFO] Task started: Blastn
[2024-01-25 20:05:21,398] [INFO] Running command: blastn -query GCF_024347615.1_ASM2434761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference/reference_markers.fasta -out GCF_024347615.1_ASM2434761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:22,149] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:22,152] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:22,152] [INFO] Target genome list was writen to GCF_024347615.1_ASM2434761v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:22,166] [INFO] Task started: fastANI
[2024-01-25 20:05:22,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg4da6556c-1ab8-4679-9a7c-39c1e044ef4a/GCF_024347615.1_ASM2434761v1_genomic.fna.gz --refList GCF_024347615.1_ASM2434761v1_genomic.fna/target_genomes.txt --output GCF_024347615.1_ASM2434761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:41,547] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:41,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:41,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:41,556] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:05:41,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:41,557] [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 splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	100.0	1948	1958	95	conclusive
Vibrio splendidus	strain=NCCB 53037	GCA_001558015.1	29497	29497	type	True	99.9782	1879	1958	95	conclusive
Vibrio splendidus	strain=DSM 19640	GCA_002737025.1	29497	29497	type	True	99.9714	1877	1958	95	conclusive
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	91.638	1408	1958	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	91.5738	1479	1958	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	91.5579	1528	1958	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	91.3995	1395	1958	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	91.3141	1357	1958	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	91.1624	1485	1958	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	90.7555	1351	1958	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	90.4163	1533	1958	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	90.3342	1486	1958	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	89.9235	1495	1958	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	86.5024	1334	1958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:41,558] [INFO] DFAST Taxonomy check result was written to GCF_024347615.1_ASM2434761v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:41,558] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:41,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:41,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference/checkm_data
[2024-01-25 20:05:41,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:41,613] [INFO] Task started: CheckM
[2024-01-25 20:05:41,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347615.1_ASM2434761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347615.1_ASM2434761v1_genomic.fna/checkm_input GCF_024347615.1_ASM2434761v1_genomic.fna/checkm_result
[2024-01-25 20:06:28,111] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:28,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:28,140] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:28,140] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:28,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347615.1_ASM2434761v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:28,141] [INFO] Task started: Blastn
[2024-01-25 20:06:28,142] [INFO] Running command: blastn -query GCF_024347615.1_ASM2434761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bc696c6-8f17-48f9-8495-7cda4827ee29/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347615.1_ASM2434761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:29,286] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:29,288] [INFO] Selected 16 target genomes.
[2024-01-25 20:06:29,289] [INFO] Target genome list was writen to GCF_024347615.1_ASM2434761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:29,307] [INFO] Task started: fastANI
[2024-01-25 20:06:29,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg4da6556c-1ab8-4679-9a7c-39c1e044ef4a/GCF_024347615.1_ASM2434761v1_genomic.fna.gz --refList GCF_024347615.1_ASM2434761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347615.1_ASM2434761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:51,006] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:51,017] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:51,017] [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_001558015.1	s__Vibrio splendidus	99.9782	1879	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.85	95.03	0.88	0.83	97	conclusive
GCF_002873455.1	s__Vibrio splendidus_J	92.6182	1513	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_000272045.2	s__Vibrio crassostreae_C	91.6501	1432	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002156525.1	s__Vibrio celticus	91.6389	1384	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	91.5814	1290	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_900089855.1	s__Vibrio atlanticus	91.3174	1356	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000272105.2	s__Vibrio splendidus_I	91.1707	1424	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014878155.1	s__Vibrio lentus	91.1511	1486	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_006333845.1	s__Vibrio tasmaniensis	90.6466	1308	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_002875945.1	s__Vibrio lentus_A	90.3849	1460	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048535.1	s__Vibrio crassostreae	90.325	1487	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_004764665.1	s__Vibrio echinoideorum	90.2879	1510	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_014879975.1	s__Vibrio bathopelagicus	89.8991	1496	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	89.8107	1393	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_000316985.1	s__Vibrio sp000316985	88.8032	1333	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394185.1	s__Vibrio sp013394185	88.6617	1511	1958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:51,018] [INFO] GTDB search result was written to GCF_024347615.1_ASM2434761v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:51,019] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:51,022] [INFO] DFAST_QC result json was written to GCF_024347615.1_ASM2434761v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:51,022] [INFO] DFAST_QC completed!
[2024-01-25 20:06:51,022] [INFO] Total running time: 0h1m46s