[2024-01-24 13:12:38,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,842] [INFO] DQC Reference Directory: /var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference
[2024-01-24 13:12:40,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,184] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,184] [INFO] Running command: gunzip -c /var/lib/cwl/stgdee58739-ce91-4519-8ca6-9aa826765e2d/GCF_001559595.1_CAIM912T.1_genomic.fna.gz | prodigal -d GCF_001559595.1_CAIM912T.1_genomic.fna/cds.fna -a GCF_001559595.1_CAIM912T.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:56,512] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:56,512] [INFO] Task started: HMMsearch
[2024-01-24 13:12:56,512] [INFO] Running command: hmmsearch --tblout GCF_001559595.1_CAIM912T.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference/reference_markers.hmm GCF_001559595.1_CAIM912T.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:56,911] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:56,913] [INFO] Found 6/6 markers.
[2024-01-24 13:12:56,969] [INFO] Query marker FASTA was written to GCF_001559595.1_CAIM912T.1_genomic.fna/markers.fasta
[2024-01-24 13:12:56,970] [INFO] Task started: Blastn
[2024-01-24 13:12:56,970] [INFO] Running command: blastn -query GCF_001559595.1_CAIM912T.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference/reference_markers.fasta -out GCF_001559595.1_CAIM912T.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:57,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:57,840] [INFO] Selected 13 target genomes.
[2024-01-24 13:12:57,840] [INFO] Target genome list was writen to GCF_001559595.1_CAIM912T.1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:57,849] [INFO] Task started: fastANI
[2024-01-24 13:12:57,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee58739-ce91-4519-8ca6-9aa826765e2d/GCF_001559595.1_CAIM912T.1_genomic.fna.gz --refList GCF_001559595.1_CAIM912T.1_genomic.fna/target_genomes.txt --output GCF_001559595.1_CAIM912T.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:09,843] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:09,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:09,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:09,857] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:09,857] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:09,857] [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
Enterovibrio nigricans	strain=DSM 22720	GCA_900167155.1	504469	504469	type	True	83.1835	991	1805	95	below_threshold
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	81.1432	737	1805	95	below_threshold
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	81.1259	723	1805	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	80.97	679	1805	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	80.9544	752	1805	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_014863865.1	2491023	2491023	type	True	80.1604	676	1805	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	80.0513	537	1805	95	below_threshold
Grimontia hollisae	strain=NCTC11640	GCA_900450635.1	673	673	type	True	80.0448	548	1805	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	78.5	119	1805	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.8439	218	1805	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	77.7078	194	1805	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	77.5474	196	1805	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	77.3635	190	1805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:09,861] [INFO] DFAST Taxonomy check result was written to GCF_001559595.1_CAIM912T.1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:09,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:09,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:09,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference/checkm_data
[2024-01-24 13:13:09,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:09,920] [INFO] Task started: CheckM
[2024-01-24 13:13:09,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001559595.1_CAIM912T.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001559595.1_CAIM912T.1_genomic.fna/checkm_input GCF_001559595.1_CAIM912T.1_genomic.fna/checkm_result
[2024-01-24 13:13:59,667] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:59,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:59,690] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:59,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:59,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001559595.1_CAIM912T.1_genomic.fna/markers.fasta)
[2024-01-24 13:13:59,691] [INFO] Task started: Blastn
[2024-01-24 13:13:59,691] [INFO] Running command: blastn -query GCF_001559595.1_CAIM912T.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabbc5c8c-3d95-4389-96f8-e7ba73ec6c09/dqc_reference/reference_markers_gtdb.fasta -out GCF_001559595.1_CAIM912T.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,724] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:00,724] [INFO] Target genome list was writen to GCF_001559595.1_CAIM912T.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:00,733] [INFO] Task started: fastANI
[2024-01-24 13:14:00,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee58739-ce91-4519-8ca6-9aa826765e2d/GCF_001559595.1_CAIM912T.1_genomic.fna.gz --refList GCF_001559595.1_CAIM912T.1_genomic.fna/target_genomes_gtdb.txt --output GCF_001559595.1_CAIM912T.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:09,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,241] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:09,241] [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_001559595.1	s__Enterovibrio coralii	100.0	1803	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167155.1	s__Enterovibrio nigricans	83.1878	990	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.93	99.93	1.00	1.00	2	-
GCF_000333895.2	s__Enterovibrio indicus	81.1582	734	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.52	96.52	0.90	0.90	2	-
GCF_011045095.1	s__Enterovibrio sedimenti	81.1168	724	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900060185.1	s__Enterovibrio marinus	80.9796	678	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900055185.1	s__Enterovibrio celer	80.9403	754	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001310415.1	s__Enterovibrio sp001310415	80.6892	700	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	-
GCF_000176515.1	s__Enterovibrio hollisae	80.049	538	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,243] [INFO] GTDB search result was written to GCF_001559595.1_CAIM912T.1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:09,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:09,246] [INFO] DFAST_QC result json was written to GCF_001559595.1_CAIM912T.1_genomic.fna/dqc_result.json
[2024-01-24 13:14:09,247] [INFO] DFAST_QC completed!
[2024-01-24 13:14:09,247] [INFO] Total running time: 0h1m30s