[2024-01-24 13:18:45,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:45,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:45,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference
[2024-01-24 13:18:46,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:46,728] [INFO] Task started: Prodigal
[2024-01-24 13:18:46,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg59a80295-b2f6-4c17-bd58-3e17ed4bb2e5/GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna.gz | prodigal -d GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/cds.fna -a GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:02,405] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:02,405] [INFO] Task started: HMMsearch
[2024-01-24 13:19:02,405] [INFO] Running command: hmmsearch --tblout GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference/reference_markers.hmm GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:02,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:02,738] [INFO] Found 6/6 markers.
[2024-01-24 13:19:02,784] [INFO] Query marker FASTA was written to GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:19:02,784] [INFO] Task started: Blastn
[2024-01-24 13:19:02,785] [INFO] Running command: blastn -query GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference/reference_markers.fasta -out GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,613] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,617] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:03,617] [INFO] Target genome list was writen to GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:19:03,624] [INFO] Task started: fastANI
[2024-01-24 13:19:03,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a80295-b2f6-4c17-bd58-3e17ed4bb2e5/GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna.gz --refList GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/target_genomes.txt --output GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:15,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:15,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:16,000] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:16,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:16,000] [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 marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	100.0	1773	1777	95	conclusive
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	90.3385	1359	1777	95	below_threshold
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	89.7668	1284	1777	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	88.8178	1353	1777	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	81.6856	749	1777	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	78.4529	171	1777	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	78.0562	158	1777	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	77.9955	138	1777	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	77.5883	115	1777	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	76.5905	54	1777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:16,002] [INFO] DFAST Taxonomy check result was written to GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:19:16,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:16,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:16,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference/checkm_data
[2024-01-24 13:19:16,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:16,058] [INFO] Task started: CheckM
[2024-01-24 13:19:16,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/checkm_input GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/checkm_result
[2024-01-24 13:20:04,447] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:04,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:04,469] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:04,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:04,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:20:04,470] [INFO] Task started: Blastn
[2024-01-24 13:20:04,470] [INFO] Running command: blastn -query GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf1ab71-32e1-4cd1-bf7d-698181f67b46/dqc_reference/reference_markers_gtdb.fasta -out GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:05,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:05,677] [INFO] Selected 7 target genomes.
[2024-01-24 13:20:05,677] [INFO] Target genome list was writen to GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:05,702] [INFO] Task started: fastANI
[2024-01-24 13:20:05,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a80295-b2f6-4c17-bd58-3e17ed4bb2e5/GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna.gz --refList GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:15,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:15,466] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:15,467] [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_900060185.1	s__Enterovibrio marinus	100.0	1773	1777	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_000333895.2	s__Enterovibrio indicus	90.3357	1359	1777	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	89.7785	1283	1777	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	88.8104	1354	1777	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	81.6903	749	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
GCA_001310415.1	s__Enterovibrio sp001310415	81.43	743	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	-
GCF_001559595.1	s__Enterovibrio coralii	80.9913	681	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:15,468] [INFO] GTDB search result was written to GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:15,469] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:15,471] [INFO] DFAST_QC result json was written to GCF_900060185.1_GmarinaCECT8713_SPAdes_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:20:15,471] [INFO] DFAST_QC completed!
[2024-01-24 13:20:15,472] [INFO] Total running time: 0h1m30s