[2024-01-24 13:01:53,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference
[2024-01-24 13:01:54,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,657] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg43b778e9-63cc-45f2-ae4a-44a69c7228da/GCF_024347595.1_ASM2434759v1_genomic.fna.gz | prodigal -d GCF_024347595.1_ASM2434759v1_genomic.fna/cds.fna -a GCF_024347595.1_ASM2434759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:12,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:12,004] [INFO] Task started: HMMsearch
[2024-01-24 13:02:12,004] [INFO] Running command: hmmsearch --tblout GCF_024347595.1_ASM2434759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference/reference_markers.hmm GCF_024347595.1_ASM2434759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:12,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:12,404] [INFO] Found 6/6 markers.
[2024-01-24 13:02:12,452] [INFO] Query marker FASTA was written to GCF_024347595.1_ASM2434759v1_genomic.fna/markers.fasta
[2024-01-24 13:02:12,453] [INFO] Task started: Blastn
[2024-01-24 13:02:12,453] [INFO] Running command: blastn -query GCF_024347595.1_ASM2434759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference/reference_markers.fasta -out GCF_024347595.1_ASM2434759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:13,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:13,250] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:13,250] [INFO] Target genome list was writen to GCF_024347595.1_ASM2434759v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:13,255] [INFO] Task started: fastANI
[2024-01-24 13:02:13,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b778e9-63cc-45f2-ae4a-44a69c7228da/GCF_024347595.1_ASM2434759v1_genomic.fna.gz --refList GCF_024347595.1_ASM2434759v1_genomic.fna/target_genomes.txt --output GCF_024347595.1_ASM2434759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:34,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:34,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:34,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:34,643] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:34,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:34,644] [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
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	100.0	1873	1885	95	conclusive
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	91.4319	1486	1885	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	91.3026	1424	1885	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	90.3904	1478	1885	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	90.3204	1424	1885	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.7711	1418	1885	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	89.7275	1366	1885	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	89.5354	1278	1885	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.3782	1497	1885	95	below_threshold
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	89.3684	1417	1885	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	88.7782	1520	1885	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	88.7542	1294	1885	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	88.6703	1340	1885	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	88.5088	1288	1885	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	88.4871	1286	1885	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	88.3187	1290	1885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,645] [INFO] DFAST Taxonomy check result was written to GCF_024347595.1_ASM2434759v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:34,646] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:34,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:34,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference/checkm_data
[2024-01-24 13:02:34,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:34,701] [INFO] Task started: CheckM
[2024-01-24 13:02:34,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347595.1_ASM2434759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347595.1_ASM2434759v1_genomic.fna/checkm_input GCF_024347595.1_ASM2434759v1_genomic.fna/checkm_result
[2024-01-24 13:03:29,196] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:29,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:29,224] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:29,224] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:29,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347595.1_ASM2434759v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:29,225] [INFO] Task started: Blastn
[2024-01-24 13:03:29,225] [INFO] Running command: blastn -query GCF_024347595.1_ASM2434759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92975029-f594-4b9a-b13a-a2ee55cc5a23/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347595.1_ASM2434759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:30,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:30,411] [INFO] Selected 16 target genomes.
[2024-01-24 13:03:30,412] [INFO] Target genome list was writen to GCF_024347595.1_ASM2434759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:30,427] [INFO] Task started: fastANI
[2024-01-24 13:03:30,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b778e9-63cc-45f2-ae4a-44a69c7228da/GCF_024347595.1_ASM2434759v1_genomic.fna.gz --refList GCF_024347595.1_ASM2434759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347595.1_ASM2434759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:50,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:50,588] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:50,588] [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_013394185.1	s__Vibrio sp013394185	96.0824	1640	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000316985.1	s__Vibrio sp000316985	94.6426	1434	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048535.1	s__Vibrio crassostreae	91.3116	1423	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_002156475.1	s__Vibrio gigantis	90.314	1425	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_000272105.2	s__Vibrio splendidus_I	90.3097	1361	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858795.1	s__Vibrio sp007858795	90.1137	1409	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272045.2	s__Vibrio crassostreae_C	89.9905	1411	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002875705.1	s__Vibrio sp002875705	89.7231	1373	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_900089765.1	s__Vibrio toranzoniae	89.4921	1256	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.37	97.69	0.93	0.89	7	-
GCF_002156455.1	s__Vibrio coralliirubri	89.3608	1418	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_001557875.1	s__Vibrio splendidus_F	89.3423	1411	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.7712	1520	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281815.1	s__Vibrio chagasii	88.5	1289	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_008801285.1	s__Vibrio kanaloae	88.452	1269	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_002954585.1	s__Vibrio chagasii_A	87.9601	1345	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_001635455.1	s__Vibrio sp001635455	87.5089	1227	1885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:50,590] [INFO] GTDB search result was written to GCF_024347595.1_ASM2434759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:50,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:50,596] [INFO] DFAST_QC result json was written to GCF_024347595.1_ASM2434759v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:50,596] [INFO] DFAST_QC completed!
[2024-01-24 13:03:50,596] [INFO] Total running time: 0h1m57s