[2024-01-24 12:31:50,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:50,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:50,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference
[2024-01-24 12:31:52,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,076] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg51418404-c47a-44f3-8af6-8c8fcacffe0c/GCF_024347635.1_ASM2434763v1_genomic.fna.gz | prodigal -d GCF_024347635.1_ASM2434763v1_genomic.fna/cds.fna -a GCF_024347635.1_ASM2434763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:04,704] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:04,705] [INFO] Task started: HMMsearch
[2024-01-24 12:32:04,705] [INFO] Running command: hmmsearch --tblout GCF_024347635.1_ASM2434763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference/reference_markers.hmm GCF_024347635.1_ASM2434763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:05,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:05,038] [INFO] Found 6/6 markers.
[2024-01-24 12:32:05,079] [INFO] Query marker FASTA was written to GCF_024347635.1_ASM2434763v1_genomic.fna/markers.fasta
[2024-01-24 12:32:05,079] [INFO] Task started: Blastn
[2024-01-24 12:32:05,080] [INFO] Running command: blastn -query GCF_024347635.1_ASM2434763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference/reference_markers.fasta -out GCF_024347635.1_ASM2434763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:05,869] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:05,875] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:05,875] [INFO] Target genome list was writen to GCF_024347635.1_ASM2434763v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:05,880] [INFO] Task started: fastANI
[2024-01-24 12:32:05,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg51418404-c47a-44f3-8af6-8c8fcacffe0c/GCF_024347635.1_ASM2434763v1_genomic.fna.gz --refList GCF_024347635.1_ASM2434763v1_genomic.fna/target_genomes.txt --output GCF_024347635.1_ASM2434763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:21,399] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:21,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:21,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:21,414] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:21,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:21,415] [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 tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	100.0	1656	1662	95	conclusive
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	99.9358	1534	1662	95	conclusive
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	94.3222	1416	1662	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	94.3112	1376	1662	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	90.7997	1375	1662	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	90.1025	1301	1662	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.8312	1339	1662	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.7803	1330	1662	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	89.4722	1347	1662	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	89.2567	1302	1662	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	89.1471	1299	1662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:21,416] [INFO] DFAST Taxonomy check result was written to GCF_024347635.1_ASM2434763v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:21,417] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:21,417] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:21,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference/checkm_data
[2024-01-24 12:32:21,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:21,467] [INFO] Task started: CheckM
[2024-01-24 12:32:21,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347635.1_ASM2434763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347635.1_ASM2434763v1_genomic.fna/checkm_input GCF_024347635.1_ASM2434763v1_genomic.fna/checkm_result
[2024-01-24 12:33:03,994] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:03,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:04,017] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:04,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:04,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347635.1_ASM2434763v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:04,018] [INFO] Task started: Blastn
[2024-01-24 12:33:04,018] [INFO] Running command: blastn -query GCF_024347635.1_ASM2434763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a7e87fc-779f-4970-84c8-47d7367c98c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347635.1_ASM2434763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:05,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:05,175] [INFO] Selected 12 target genomes.
[2024-01-24 12:33:05,175] [INFO] Target genome list was writen to GCF_024347635.1_ASM2434763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:05,185] [INFO] Task started: fastANI
[2024-01-24 12:33:05,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg51418404-c47a-44f3-8af6-8c8fcacffe0c/GCF_024347635.1_ASM2434763v1_genomic.fna.gz --refList GCF_024347635.1_ASM2434763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347635.1_ASM2434763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:20,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:20,244] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:20,244] [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_006333845.1	s__Vibrio tasmaniensis	99.9358	1534	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	conclusive
GCF_900089855.1	s__Vibrio atlanticus	94.3112	1376	1662	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	94.1463	1306	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_014878155.1	s__Vibrio lentus	90.1052	1301	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_002873455.1	s__Vibrio splendidus_J	89.9354	1324	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_000272045.2	s__Vibrio crassostreae_C	89.7852	1288	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002156455.1	s__Vibrio coralliirubri	89.7353	1265	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_002875945.1	s__Vibrio lentus_A	89.5653	1277	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272105.2	s__Vibrio splendidus_I	89.4533	1239	1662	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	89.2859	1268	1662	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	89.2668	1302	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_014879975.1	s__Vibrio bathopelagicus	89.1612	1301	1662	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 12:33:20,246] [INFO] GTDB search result was written to GCF_024347635.1_ASM2434763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:20,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:20,250] [INFO] DFAST_QC result json was written to GCF_024347635.1_ASM2434763v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:20,250] [INFO] DFAST_QC completed!
[2024-01-24 12:33:20,250] [INFO] Total running time: 0h1m29s