[2024-01-24 13:28:13,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference
[2024-01-24 13:28:15,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:15,168] [INFO] Task started: Prodigal
[2024-01-24 13:28:15,169] [INFO] Running command: gunzip -c /var/lib/cwl/stg541e3f77-3992-4776-9874-8f9a44aea461/GCF_014879975.1_ASM1487997v1_genomic.fna.gz | prodigal -d GCF_014879975.1_ASM1487997v1_genomic.fna/cds.fna -a GCF_014879975.1_ASM1487997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:28,849] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:28,850] [INFO] Task started: HMMsearch
[2024-01-24 13:28:28,850] [INFO] Running command: hmmsearch --tblout GCF_014879975.1_ASM1487997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference/reference_markers.hmm GCF_014879975.1_ASM1487997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:29,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:29,181] [INFO] Found 6/6 markers.
[2024-01-24 13:28:29,238] [INFO] Query marker FASTA was written to GCF_014879975.1_ASM1487997v1_genomic.fna/markers.fasta
[2024-01-24 13:28:29,239] [INFO] Task started: Blastn
[2024-01-24 13:28:29,239] [INFO] Running command: blastn -query GCF_014879975.1_ASM1487997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference/reference_markers.fasta -out GCF_014879975.1_ASM1487997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:30,059] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:30,063] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:30,063] [INFO] Target genome list was writen to GCF_014879975.1_ASM1487997v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:30,079] [INFO] Task started: fastANI
[2024-01-24 13:28:30,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg541e3f77-3992-4776-9874-8f9a44aea461/GCF_014879975.1_ASM1487997v1_genomic.fna.gz --refList GCF_014879975.1_ASM1487997v1_genomic.fna/target_genomes.txt --output GCF_014879975.1_ASM1487997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:51,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:51,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:51,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:51,487] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:51,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:51,487] [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 bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	100.0	1879	1888	95	conclusive
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	92.2063	1495	1888	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	90.1672	1489	1888	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	89.9444	1488	1888	95	below_threshold
Vibrio splendidus	strain=DSM 19640	GCA_002737025.1	29497	29497	type	True	89.9016	1442	1888	95	below_threshold
Vibrio splendidus	strain=NCCB 53037	GCA_001558015.1	29497	29497	type	True	89.8677	1453	1888	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	89.1772	1332	1888	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	89.0887	1289	1888	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	89.0117	1314	1888	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	88.9631	1461	1888	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	88.9105	1259	1888	95	below_threshold
Vibrio echinoideorum	strain=NFH.MB010	GCA_004764665.1	2100116	2100116	type	True	88.7777	1448	1888	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	88.3676	1337	1888	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	87.9636	1251	1888	95	below_threshold
Vibrio toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	87.8197	1235	1888	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	87.7875	1228	1888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:51,489] [INFO] DFAST Taxonomy check result was written to GCF_014879975.1_ASM1487997v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:51,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:51,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:51,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference/checkm_data
[2024-01-24 13:28:51,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:51,552] [INFO] Task started: CheckM
[2024-01-24 13:28:51,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014879975.1_ASM1487997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014879975.1_ASM1487997v1_genomic.fna/checkm_input GCF_014879975.1_ASM1487997v1_genomic.fna/checkm_result
[2024-01-24 13:29:36,787] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:36,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:36,820] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:36,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:36,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014879975.1_ASM1487997v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:36,821] [INFO] Task started: Blastn
[2024-01-24 13:29:36,821] [INFO] Running command: blastn -query GCF_014879975.1_ASM1487997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e306974-6748-4091-8226-053d28174226/dqc_reference/reference_markers_gtdb.fasta -out GCF_014879975.1_ASM1487997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:38,011] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:38,015] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:38,015] [INFO] Target genome list was writen to GCF_014879975.1_ASM1487997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:38,037] [INFO] Task started: fastANI
[2024-01-24 13:29:38,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg541e3f77-3992-4776-9874-8f9a44aea461/GCF_014879975.1_ASM1487997v1_genomic.fna.gz --refList GCF_014879975.1_ASM1487997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014879975.1_ASM1487997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:56,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:56,017] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:56,017] [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_014879975.1	s__Vibrio bathopelagicus	100.0	1880	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002875945.1	s__Vibrio lentus_A	93.4013	1477	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014878155.1	s__Vibrio lentus	92.2018	1495	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_001558015.1	s__Vibrio splendidus	89.8783	1452	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.85	95.03	0.88	0.83	97	-
GCF_002873455.1	s__Vibrio splendidus_J	89.3831	1372	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_900089855.1	s__Vibrio atlanticus	89.1114	1286	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	89.0181	1247	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_006333845.1	s__Vibrio tasmaniensis	88.9214	1258	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_013394185.1	s__Vibrio sp013394185	88.8517	1458	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000272045.2	s__Vibrio crassostreae_C	88.8191	1360	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_004764665.1	s__Vibrio echinoideorum	88.7777	1448	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_000316985.1	s__Vibrio sp000316985	88.6495	1325	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144905.1	s__Vibrio cyclitrophicus	88.3031	1360	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.18	99.01	0.95	0.91	87	-
GCF_900089765.1	s__Vibrio toranzoniae	87.795	1227	1888	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 13:29:56,019] [INFO] GTDB search result was written to GCF_014879975.1_ASM1487997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:56,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:56,023] [INFO] DFAST_QC result json was written to GCF_014879975.1_ASM1487997v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:56,023] [INFO] DFAST_QC completed!
[2024-01-24 13:29:56,023] [INFO] Total running time: 0h1m42s