[2024-01-24 13:40:40,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:40,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:40,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference
[2024-01-24 13:40:41,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:41,812] [INFO] Task started: Prodigal
[2024-01-24 13:40:41,812] [INFO] Running command: gunzip -c /var/lib/cwl/stge550bb7e-9897-4cf6-8fa8-8936cee775f7/GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna.gz | prodigal -d GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/cds.fna -a GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,083] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,083] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,084] [INFO] Running command: hmmsearch --tblout GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference/reference_markers.hmm GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:54,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:54,485] [INFO] Found 6/6 markers.
[2024-01-24 13:40:54,535] [INFO] Query marker FASTA was written to GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:40:54,536] [INFO] Task started: Blastn
[2024-01-24 13:40:54,536] [INFO] Running command: blastn -query GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference/reference_markers.fasta -out GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,420] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,423] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:55,424] [INFO] Target genome list was writen to GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:40:55,434] [INFO] Task started: fastANI
[2024-01-24 13:40:55,435] [INFO] Running command: fastANI --query /var/lib/cwl/stge550bb7e-9897-4cf6-8fa8-8936cee775f7/GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna.gz --refList GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/target_genomes.txt --output GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,246] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,258] [INFO] Found 13 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:41:13,258] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:41:13,258] [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 celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	100.0	1683	1701	95	inconclusive
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	99.9922	1696	1701	95	inconclusive
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	99.9555	1624	1701	95	inconclusive
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	95.2994	1334	1701	95	inconclusive
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	95.1759	1385	1701	95	inconclusive
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	92.5957	1345	1701	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	92.511	1365	1701	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	90.3776	1289	1701	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	89.7639	1279	1701	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	89.6287	1207	1701	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	89.5676	1215	1701	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	88.2739	1209	1701	95	below_threshold
Vibrio toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	88.2153	1215	1701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,260] [INFO] DFAST Taxonomy check result was written to GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference/checkm_data
[2024-01-24 13:41:13,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,328] [INFO] Task started: CheckM
[2024-01-24 13:41:13,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/checkm_input GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/checkm_result
[2024-01-24 13:41:54,607] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:54,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:54,632] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:54,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:54,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:41:54,633] [INFO] Task started: Blastn
[2024-01-24 13:41:54,633] [INFO] Running command: blastn -query GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4dfbb7-18bd-41b1-a8f1-97db5b284eeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:55,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:55,859] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:55,859] [INFO] Target genome list was writen to GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:55,868] [INFO] Task started: fastANI
[2024-01-24 13:41:55,869] [INFO] Running command: fastANI --query /var/lib/cwl/stge550bb7e-9897-4cf6-8fa8-8936cee775f7/GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna.gz --refList GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:11,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,528] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:42:11,528] [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_002156525.1	s__Vibrio celticus	99.9555	1624	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	inconclusive
GCF_002156455.1	s__Vibrio coralliirubri	95.2989	1334	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	inconclusive
GCF_000272045.2	s__Vibrio crassostreae_C	94.7723	1395	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000272105.2	s__Vibrio splendidus_I	94.1867	1338	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557875.1	s__Vibrio splendidus_F	92.8482	1356	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_001048535.1	s__Vibrio crassostreae	92.6047	1344	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_007858795.1	s__Vibrio sp007858795	92.0349	1352	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	91.5901	1315	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_002156475.1	s__Vibrio gigantis	90.6647	1313	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_008801285.1	s__Vibrio kanaloae	89.6167	1208	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.8326	1305	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089765.1	s__Vibrio toranzoniae	88.2739	1209	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.37	97.69	0.93	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,530] [INFO] GTDB search result was written to GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:11,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:11,535] [INFO] DFAST_QC result json was written to GCF_900089965.1_VcelticusCECT7224_Velvet_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:42:11,535] [INFO] DFAST_QC completed!
[2024-01-24 13:42:11,535] [INFO] Total running time: 0h1m31s