[2024-01-24 11:35:11,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,959] [INFO] DQC Reference Directory: /var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference
[2024-01-24 11:35:14,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:14,432] [INFO] Task started: Prodigal
[2024-01-24 11:35:14,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg89cf132d-403e-4509-9214-cdac059d8b27/GCF_019209835.1_ASM1920983v1_genomic.fna.gz | prodigal -d GCF_019209835.1_ASM1920983v1_genomic.fna/cds.fna -a GCF_019209835.1_ASM1920983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:30,699] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:30,700] [INFO] Task started: HMMsearch
[2024-01-24 11:35:30,700] [INFO] Running command: hmmsearch --tblout GCF_019209835.1_ASM1920983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference/reference_markers.hmm GCF_019209835.1_ASM1920983v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:31,018] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:31,019] [INFO] Found 6/6 markers.
[2024-01-24 11:35:31,071] [INFO] Query marker FASTA was written to GCF_019209835.1_ASM1920983v1_genomic.fna/markers.fasta
[2024-01-24 11:35:31,071] [INFO] Task started: Blastn
[2024-01-24 11:35:31,071] [INFO] Running command: blastn -query GCF_019209835.1_ASM1920983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference/reference_markers.fasta -out GCF_019209835.1_ASM1920983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:31,982] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:31,986] [INFO] Selected 12 target genomes.
[2024-01-24 11:35:31,986] [INFO] Target genome list was writen to GCF_019209835.1_ASM1920983v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:31,991] [INFO] Task started: fastANI
[2024-01-24 11:35:31,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg89cf132d-403e-4509-9214-cdac059d8b27/GCF_019209835.1_ASM1920983v1_genomic.fna.gz --refList GCF_019209835.1_ASM1920983v1_genomic.fna/target_genomes.txt --output GCF_019209835.1_ASM1920983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:43,351] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:43,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:43,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:43,363] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:43,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:43,363] [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
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	81.7911	828	1782	95	below_threshold
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	81.7216	822	1782	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	81.6825	760	1782	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	81.6062	823	1782	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	80.9514	703	1782	95	below_threshold
Enterovibrio nigricans	strain=DSM 22720	GCA_900167155.1	504469	504469	type	True	80.4277	551	1782	95	below_threshold
Enterovibrio calviensis	strain=DSM 14347	GCA_000621165.1	91359	91359	type	True	79.6909	606	1782	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	78.2556	210	1782	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	78.2259	129	1782	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.0947	177	1782	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.9332	239	1782	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	77.7891	221	1782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:43,365] [INFO] DFAST Taxonomy check result was written to GCF_019209835.1_ASM1920983v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:43,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:43,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:43,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference/checkm_data
[2024-01-24 11:35:43,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:43,417] [INFO] Task started: CheckM
[2024-01-24 11:35:43,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019209835.1_ASM1920983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019209835.1_ASM1920983v1_genomic.fna/checkm_input GCF_019209835.1_ASM1920983v1_genomic.fna/checkm_result
[2024-01-24 11:36:32,641] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:32,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:32,666] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:32,666] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:32,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019209835.1_ASM1920983v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:32,667] [INFO] Task started: Blastn
[2024-01-24 11:36:32,667] [INFO] Running command: blastn -query GCF_019209835.1_ASM1920983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81ae4d0-6b88-4cf2-99ca-7f0ce783d4c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019209835.1_ASM1920983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:33,980] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:33,984] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:33,985] [INFO] Target genome list was writen to GCF_019209835.1_ASM1920983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:33,991] [INFO] Task started: fastANI
[2024-01-24 11:36:33,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg89cf132d-403e-4509-9214-cdac059d8b27/GCF_019209835.1_ASM1920983v1_genomic.fna.gz --refList GCF_019209835.1_ASM1920983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019209835.1_ASM1920983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:42,897] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:42,913] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:42,913] [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
GCA_001310415.1	s__Enterovibrio sp001310415	96.6785	1571	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	conclusive
GCF_000333895.2	s__Enterovibrio indicus	81.7964	829	1782	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	81.7294	819	1782	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	81.676	760	1782	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	81.6209	824	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176515.1	s__Enterovibrio hollisae	80.9451	704	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
GCF_001559595.1	s__Enterovibrio coralii	80.8703	697	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167155.1	s__Enterovibrio nigricans	80.4317	552	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.93	99.93	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:42,915] [INFO] GTDB search result was written to GCF_019209835.1_ASM1920983v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:42,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:42,920] [INFO] DFAST_QC result json was written to GCF_019209835.1_ASM1920983v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:42,920] [INFO] DFAST_QC completed!
[2024-01-24 11:36:42,920] [INFO] Total running time: 0h1m31s