[2024-01-24 13:42:57,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference
[2024-01-24 13:42:58,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,950] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgf58f10cd-94e1-44ef-9cc9-45a1475a46c1/GCF_004116385.1_CAIM600T.1_genomic.fna.gz | prodigal -d GCF_004116385.1_CAIM600T.1_genomic.fna/cds.fna -a GCF_004116385.1_CAIM600T.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:12,227] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:12,228] [INFO] Task started: HMMsearch
[2024-01-24 13:43:12,228] [INFO] Running command: hmmsearch --tblout GCF_004116385.1_CAIM600T.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference/reference_markers.hmm GCF_004116385.1_CAIM600T.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:12,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:12,520] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf58f10cd-94e1-44ef-9cc9-45a1475a46c1/GCF_004116385.1_CAIM600T.1_genomic.fna.gz]
[2024-01-24 13:43:12,566] [INFO] Query marker FASTA was written to GCF_004116385.1_CAIM600T.1_genomic.fna/markers.fasta
[2024-01-24 13:43:12,567] [INFO] Task started: Blastn
[2024-01-24 13:43:12,567] [INFO] Running command: blastn -query GCF_004116385.1_CAIM600T.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference/reference_markers.fasta -out GCF_004116385.1_CAIM600T.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:13,353] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:13,358] [INFO] Selected 19 target genomes.
[2024-01-24 13:43:13,358] [INFO] Target genome list was writen to GCF_004116385.1_CAIM600T.1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:13,370] [INFO] Task started: fastANI
[2024-01-24 13:43:13,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgf58f10cd-94e1-44ef-9cc9-45a1475a46c1/GCF_004116385.1_CAIM600T.1_genomic.fna.gz --refList GCF_004116385.1_CAIM600T.1_genomic.fna/target_genomes.txt --output GCF_004116385.1_CAIM600T.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:28,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:28,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:28,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:28,061] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:43:28,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:43:28,061] [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	79.1166	277	1711	95	below_threshold
Grimontia hollisae	strain=NCTC11640	GCA_900450635.1	673	673	type	True	79.0096	235	1711	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	78.8894	242	1711	95	below_threshold
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	78.8503	272	1711	95	below_threshold
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	78.8414	287	1711	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	78.7754	268	1711	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_014863865.1	2491023	2491023	type	True	78.7607	217	1711	95	below_threshold
Enterovibrio norvegicus	strain=DSM 15893	GCA_900115495.1	188144	188144	type	True	78.5138	226	1711	95	below_threshold
Enterovibrio calviensis	strain=DSM 14347	GCA_000621165.1	91359	91359	type	True	78.3056	229	1711	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.2764	107	1711	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	78.2663	95	1711	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	78.1092	97	1711	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.0961	128	1711	95	below_threshold
Photobacterium arenosum	strain=CAU 1568	GCA_014841115.1	2774143	2774143	type	True	78.0013	129	1711	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	77.91	123	1711	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	77.8253	101	1711	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	77.4873	97	1711	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.1299	52	1711	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:28,063] [INFO] DFAST Taxonomy check result was written to GCF_004116385.1_CAIM600T.1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:28,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:28,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:28,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference/checkm_data
[2024-01-24 13:43:28,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:28,118] [INFO] Task started: CheckM
[2024-01-24 13:43:28,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116385.1_CAIM600T.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116385.1_CAIM600T.1_genomic.fna/checkm_input GCF_004116385.1_CAIM600T.1_genomic.fna/checkm_result
[2024-01-24 13:44:11,182] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:11,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:11,204] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:11,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:11,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116385.1_CAIM600T.1_genomic.fna/markers.fasta)
[2024-01-24 13:44:11,205] [INFO] Task started: Blastn
[2024-01-24 13:44:11,206] [INFO] Running command: blastn -query GCF_004116385.1_CAIM600T.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfce923b0-e291-42af-a023-a7146a782fbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116385.1_CAIM600T.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:12,281] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:12,286] [INFO] Selected 11 target genomes.
[2024-01-24 13:44:12,286] [INFO] Target genome list was writen to GCF_004116385.1_CAIM600T.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:12,309] [INFO] Task started: fastANI
[2024-01-24 13:44:12,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgf58f10cd-94e1-44ef-9cc9-45a1475a46c1/GCF_004116385.1_CAIM600T.1_genomic.fna.gz --refList GCF_004116385.1_CAIM600T.1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116385.1_CAIM600T.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:22,279] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:22,293] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:22,294] [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_004116385.1	s__Enterovibrio sp004116385	100.0	1689	1711	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_001707825.1	s__Enterovibrio pacificus	80.7752	567	1711	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	79.1306	277	1711	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	78.9564	235	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	-
GCF_000333895.2	s__Enterovibrio indicus	78.841	287	1711	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	78.8215	272	1711	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	78.8004	267	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286835.2	s__Enterovibrio norvegicus_A	78.6333	219	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.02	98.98	0.97	0.97	3	-
GCF_001559595.1	s__Enterovibrio coralii	78.5745	269	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938225.1	s__Vibrio ponticus	78.0702	100	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_003350325.1	s__Vibrio rhodolitus	77.4172	101	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:22,296] [INFO] GTDB search result was written to GCF_004116385.1_CAIM600T.1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:22,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:22,300] [INFO] DFAST_QC result json was written to GCF_004116385.1_CAIM600T.1_genomic.fna/dqc_result.json
[2024-01-24 13:44:22,300] [INFO] DFAST_QC completed!
[2024-01-24 13:44:22,300] [INFO] Total running time: 0h1m25s