[2024-01-24 13:17:14,035] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,036] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,037] [INFO] DQC Reference Directory: /var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference
[2024-01-24 13:17:15,314] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,315] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,315] [INFO] Running command: gunzip -c /var/lib/cwl/stg71e873ec-06b0-458e-83a8-9e35d585d514/GCF_002906655.1_ASM290665v1_genomic.fna.gz | prodigal -d GCF_002906655.1_ASM290665v1_genomic.fna/cds.fna -a GCF_002906655.1_ASM290665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:31,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:31,135] [INFO] Task started: HMMsearch
[2024-01-24 13:17:31,135] [INFO] Running command: hmmsearch --tblout GCF_002906655.1_ASM290665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference/reference_markers.hmm GCF_002906655.1_ASM290665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:31,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:31,461] [INFO] Found 6/6 markers.
[2024-01-24 13:17:31,509] [INFO] Query marker FASTA was written to GCF_002906655.1_ASM290665v1_genomic.fna/markers.fasta
[2024-01-24 13:17:31,509] [INFO] Task started: Blastn
[2024-01-24 13:17:31,509] [INFO] Running command: blastn -query GCF_002906655.1_ASM290665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference/reference_markers.fasta -out GCF_002906655.1_ASM290665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:32,355] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:32,359] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:32,359] [INFO] Target genome list was writen to GCF_002906655.1_ASM290665v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:32,364] [INFO] Task started: fastANI
[2024-01-24 13:17:32,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg71e873ec-06b0-458e-83a8-9e35d585d514/GCF_002906655.1_ASM290665v1_genomic.fna.gz --refList GCF_002906655.1_ASM290665v1_genomic.fna/target_genomes.txt --output GCF_002906655.1_ASM290665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:51,107] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:51,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:51,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:51,128] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:51,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:51,128] [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 hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	100.0	1867	1869	95	conclusive
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	99.9829	1786	1869	95	conclusive
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	89.7837	1471	1869	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	88.1781	1258	1869	95	below_threshold
Vibrio harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	87.873	1432	1869	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	87.8067	1363	1869	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	87.7439	1388	1869	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	87.508	1228	1869	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	83.9157	1093	1869	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.4036	849	1869	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.5903	441	1869	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.5594	438	1869	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	80.0524	516	1869	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	80.0468	593	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:51,130] [INFO] DFAST Taxonomy check result was written to GCF_002906655.1_ASM290665v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:51,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:51,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:51,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference/checkm_data
[2024-01-24 13:17:51,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:51,188] [INFO] Task started: CheckM
[2024-01-24 13:17:51,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002906655.1_ASM290665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002906655.1_ASM290665v1_genomic.fna/checkm_input GCF_002906655.1_ASM290665v1_genomic.fna/checkm_result
[2024-01-24 13:18:39,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:39,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:39,712] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:39,713] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:39,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002906655.1_ASM290665v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:39,714] [INFO] Task started: Blastn
[2024-01-24 13:18:39,714] [INFO] Running command: blastn -query GCF_002906655.1_ASM290665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1cbcb2f-08d8-4fa7-8252-74a6e54966ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_002906655.1_ASM290665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:40,902] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:40,905] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:40,906] [INFO] Target genome list was writen to GCF_002906655.1_ASM290665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:40,923] [INFO] Task started: fastANI
[2024-01-24 13:18:40,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg71e873ec-06b0-458e-83a8-9e35d585d514/GCF_002906655.1_ASM290665v1_genomic.fna.gz --refList GCF_002906655.1_ASM290665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002906655.1_ASM290665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:54,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:54,125] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:54,126] [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_002906655.1	s__Vibrio hyugaensis	100.0	1867	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	conclusive
GCF_000400365.1	s__Vibrio jasicida	94.3334	1585	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_000817815.1	s__Vibrio owensii	89.8054	1467	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002163755.1	s__Vibrio campbellii	88.287	1344	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001591145.1	s__Vibrio harveyi	87.732	1389	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_002741985.1	s__Vibrio rotiferianus	87.4961	1230	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_003544875.1	s__Vibrio alfacsensis	84.9907	1055	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.49	96.49	0.89	0.89	2	-
GCF_000171815.1	s__Vibrio sp000171815	84.3487	914	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460535.1	s__Vibrio parahaemolyticus	83.8984	1096	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:54,127] [INFO] GTDB search result was written to GCF_002906655.1_ASM290665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:54,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:54,130] [INFO] DFAST_QC result json was written to GCF_002906655.1_ASM290665v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:54,130] [INFO] DFAST_QC completed!
[2024-01-24 13:18:54,131] [INFO] Total running time: 0h1m40s