[2024-01-25 18:44:05,676] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference
[2024-01-25 18:44:06,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,867] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e84e50e-4d00-4b41-a32a-3c4998799a4d/GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna.gz | prodigal -d GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/cds.fna -a GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:18,239] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:18,240] [INFO] Task started: HMMsearch
[2024-01-25 18:44:18,240] [INFO] Running command: hmmsearch --tblout GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference/reference_markers.hmm GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:18,560] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:18,561] [INFO] Found 6/6 markers.
[2024-01-25 18:44:18,610] [INFO] Query marker FASTA was written to GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/markers.fasta
[2024-01-25 18:44:18,610] [INFO] Task started: Blastn
[2024-01-25 18:44:18,610] [INFO] Running command: blastn -query GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference/reference_markers.fasta -out GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:19,313] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:19,315] [INFO] Selected 8 target genomes.
[2024-01-25 18:44:19,316] [INFO] Target genome list was writen to GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/target_genomes.txt
[2024-01-25 18:44:19,318] [INFO] Task started: fastANI
[2024-01-25 18:44:19,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e84e50e-4d00-4b41-a32a-3c4998799a4d/GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna.gz --refList GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/target_genomes.txt --output GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:29,713] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:29,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:29,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:29,721] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:29,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:29,721] [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 spartinae	strain=CECT 9026	GCA_900149295.1	1918945	1918945	type	True	100.0	1674	1676	95	conclusive
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	99.999	1674	1676	95	conclusive
Vibrio gazogenes	strain=DSM 21264	GCA_900129185.1	687	687	type	True	91.9828	1294	1676	95	below_threshold
Vibrio gazogenes	strain=ATCC 29988	GCA_024346915.1	687	687	type	True	91.9049	1325	1676	95	below_threshold
Vibrio gazogenes	strain=PB1	GCA_023920225.1	687	687	type	True	91.8926	1332	1676	95	below_threshold
Vibrio gazogenes	strain=type strain: CECT 5068	GCA_900163915.1	687	687	type	True	91.6301	1057	1676	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	86.0476	1224	1676	95	below_threshold
Vibrio mangrovi	strain=CECT 7927	GCA_024346955.1	474394	474394	type	True	81.4804	926	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:29,723] [INFO] DFAST Taxonomy check result was written to GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/tc_result.tsv
[2024-01-25 18:44:29,723] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:29,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:29,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference/checkm_data
[2024-01-25 18:44:29,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:29,776] [INFO] Task started: CheckM
[2024-01-25 18:44:29,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/checkm_input GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/checkm_result
[2024-01-25 18:45:08,087] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:08,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:08,107] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:08,108] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:08,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/markers.fasta)
[2024-01-25 18:45:08,108] [INFO] Task started: Blastn
[2024-01-25 18:45:08,108] [INFO] Running command: blastn -query GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b528799-33e7-4c46-a5c9-e9816d0b33ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:09,210] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:09,214] [INFO] Selected 6 target genomes.
[2024-01-25 18:45:09,214] [INFO] Target genome list was writen to GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:09,222] [INFO] Task started: fastANI
[2024-01-25 18:45:09,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e84e50e-4d00-4b41-a32a-3c4998799a4d/GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna.gz --refList GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:17,445] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:17,450] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:17,450] [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_900149295.1	s__Vibrio spartinae	100.0	1674	1676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.28	99.28	0.90	0.90	2	conclusive
GCF_900129185.1	s__Vibrio gazogenes	91.9855	1294	1676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	-
GCF_002196515.1	s__Vibrio gazogenes_A	91.5006	1304	1676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001506075.1	s__Vibrio sp001506075	88.5961	1285	1676	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	86.8041	1223	1676	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	85.9403	1214	1676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:17,453] [INFO] GTDB search result was written to GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:17,453] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:17,456] [INFO] DFAST_QC result json was written to GCF_900149295.1_V.spartinae_CECT9026T_Velvet_Prokka_genomic.fna/dqc_result.json
[2024-01-25 18:45:17,456] [INFO] DFAST_QC completed!
[2024-01-25 18:45:17,456] [INFO] Total running time: 0h1m12s