[2024-01-24 15:27:41,307] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference
[2024-01-24 15:27:43,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,882] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stge0bddacc-c612-421e-b2f9-e358291996f4/GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/cds.fna -a GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:56,800] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:56,801] [INFO] Task started: HMMsearch
[2024-01-24 15:27:56,801] [INFO] Running command: hmmsearch --tblout GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference/reference_markers.hmm GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:57,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:57,152] [INFO] Found 6/6 markers.
[2024-01-24 15:27:57,199] [INFO] Query marker FASTA was written to GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:27:57,199] [INFO] Task started: Blastn
[2024-01-24 15:27:57,199] [INFO] Running command: blastn -query GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference/reference_markers.fasta -out GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:58,045] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:58,051] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:58,051] [INFO] Target genome list was writen to GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:27:58,058] [INFO] Task started: fastANI
[2024-01-24 15:27:58,058] [INFO] Running command: fastANI --query /var/lib/cwl/stge0bddacc-c612-421e-b2f9-e358291996f4/GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna.gz --refList GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:12,453] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:12,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:12,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:12,467] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:12,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:12,468] [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	100.0	1542	1555	95	conclusive
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	80.4973	571	1555	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	80.467	566	1555	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	80.4658	556	1555	95	below_threshold
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	80.4543	553	1555	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_004120195.1	2491023	2491023	type	True	80.3474	541	1555	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_014863865.1	2491023	2491023	type	True	80.3412	542	1555	95	below_threshold
Enterovibrio calviensis	strain=DSM 14347	GCA_000621165.1	91359	91359	type	True	80.1819	572	1555	95	below_threshold
Enterovibrio norvegicus	strain=DSM 15893	GCA_900115495.1	188144	188144	type	True	80.144	525	1555	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	79.754	471	1555	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.018	155	1555	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	77.9392	116	1555	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	77.9312	146	1555	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	77.8809	133	1555	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	77.7792	77	1555	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:12,470] [INFO] DFAST Taxonomy check result was written to GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:28:12,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:12,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:12,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference/checkm_data
[2024-01-24 15:28:12,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:12,520] [INFO] Task started: CheckM
[2024-01-24 15:28:12,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/checkm_input GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:28:54,759] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:54,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:54,785] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:54,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:54,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:28:54,786] [INFO] Task started: Blastn
[2024-01-24 15:28:54,786] [INFO] Running command: blastn -query GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg546e6d45-1341-4693-a169-3623d3f3128b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:56,026] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:56,030] [INFO] Selected 11 target genomes.
[2024-01-24 15:28:56,031] [INFO] Target genome list was writen to GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:56,044] [INFO] Task started: fastANI
[2024-01-24 15:28:56,045] [INFO] Running command: fastANI --query /var/lib/cwl/stge0bddacc-c612-421e-b2f9-e358291996f4/GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna.gz --refList GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:07,569] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:07,589] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:07,589] [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_900167155.1	s__Enterovibrio nigricans	100.0	1542	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.93	99.93	1.00	1.00	2	conclusive
GCF_001559595.1	s__Enterovibrio coralii	83.3371	990	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333895.2	s__Enterovibrio indicus	80.4929	572	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.52	96.52	0.90	0.90	2	-
GCF_900055185.1	s__Enterovibrio celer	80.4662	567	1555	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	80.4595	557	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045095.1	s__Enterovibrio sedimenti	80.4543	553	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004120195.1	s__Enterovibrio baiacu	80.3506	540	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000621165.1	s__Enterovibrio calviensis	80.1932	572	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115495.1	s__Enterovibrio norvegicus	80.1547	523	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	97.84	95.33	0.92	0.87	14	-
GCA_001310415.1	s__Enterovibrio sp001310415	80.0647	565	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	-
GCF_000286835.2	s__Enterovibrio norvegicus_A	80.0529	564	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.02	98.98	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:07,591] [INFO] GTDB search result was written to GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:07,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:07,598] [INFO] DFAST_QC result json was written to GCF_900167155.1_IMG-taxon_2568526010_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:29:07,598] [INFO] DFAST_QC completed!
[2024-01-24 15:29:07,598] [INFO] Total running time: 0h1m26s