[2024-01-24 12:40:20,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,705] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference
[2024-01-24 12:40:21,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,905] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg20be5af6-eb26-41bc-984a-29f6320d5eed/GCF_024347575.1_ASM2434757v1_genomic.fna.gz | prodigal -d GCF_024347575.1_ASM2434757v1_genomic.fna/cds.fna -a GCF_024347575.1_ASM2434757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:34,558] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:34,558] [INFO] Task started: HMMsearch
[2024-01-24 12:40:34,559] [INFO] Running command: hmmsearch --tblout GCF_024347575.1_ASM2434757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference/reference_markers.hmm GCF_024347575.1_ASM2434757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:34,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:34,846] [INFO] Found 6/6 markers.
[2024-01-24 12:40:34,885] [INFO] Query marker FASTA was written to GCF_024347575.1_ASM2434757v1_genomic.fna/markers.fasta
[2024-01-24 12:40:34,886] [INFO] Task started: Blastn
[2024-01-24 12:40:34,886] [INFO] Running command: blastn -query GCF_024347575.1_ASM2434757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference/reference_markers.fasta -out GCF_024347575.1_ASM2434757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:35,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:35,696] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:35,697] [INFO] Target genome list was writen to GCF_024347575.1_ASM2434757v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:35,701] [INFO] Task started: fastANI
[2024-01-24 12:40:35,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg20be5af6-eb26-41bc-984a-29f6320d5eed/GCF_024347575.1_ASM2434757v1_genomic.fna.gz --refList GCF_024347575.1_ASM2434757v1_genomic.fna/target_genomes.txt --output GCF_024347575.1_ASM2434757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:49,463] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:49,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:49,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:49,482] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:49,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:49,483] [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 pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	100.0	1645	1653	95	conclusive
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	88.3453	1279	1653	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	83.4712	898	1653	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	83.3531	906	1653	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	83.299	861	1653	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	83.2165	888	1653	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	83.1825	871	1653	95	below_threshold
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	82.9273	833	1653	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	82.7044	831	1653	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	82.5876	822	1653	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	82.5607	831	1653	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	82.3636	799	1653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:49,484] [INFO] DFAST Taxonomy check result was written to GCF_024347575.1_ASM2434757v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:49,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:49,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:49,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference/checkm_data
[2024-01-24 12:40:49,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:49,532] [INFO] Task started: CheckM
[2024-01-24 12:40:49,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347575.1_ASM2434757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347575.1_ASM2434757v1_genomic.fna/checkm_input GCF_024347575.1_ASM2434757v1_genomic.fna/checkm_result
[2024-01-24 12:41:31,283] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:31,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:31,303] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:31,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:31,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347575.1_ASM2434757v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:31,304] [INFO] Task started: Blastn
[2024-01-24 12:41:31,304] [INFO] Running command: blastn -query GCF_024347575.1_ASM2434757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5de4fc3-91a8-444c-b541-6abb646f1ac1/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347575.1_ASM2434757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:32,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:32,485] [INFO] Selected 14 target genomes.
[2024-01-24 12:41:32,485] [INFO] Target genome list was writen to GCF_024347575.1_ASM2434757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:32,493] [INFO] Task started: fastANI
[2024-01-24 12:41:32,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg20be5af6-eb26-41bc-984a-29f6320d5eed/GCF_024347575.1_ASM2434757v1_genomic.fna.gz --refList GCF_024347575.1_ASM2434757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347575.1_ASM2434757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:47,457] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:47,474] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:47,475] [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_000695685.1	s__Vibrio fortis	91.668	1322	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_013394185.1	s__Vibrio sp013394185	83.3888	875	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002954585.1	s__Vibrio chagasii_A	83.3212	875	1653	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	83.3021	804	1653	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	83.1908	870	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCA_000169995.1	s__Vibrio sp000169995	83.0872	836	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156455.1	s__Vibrio coralliirubri	82.9133	835	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_000272105.2	s__Vibrio splendidus_I	82.7952	833	1653	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	82.7814	855	1653	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	82.7121	849	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_002875945.1	s__Vibrio lentus_A	82.4836	852	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006333845.1	s__Vibrio tasmaniensis	82.3524	799	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_004764665.1	s__Vibrio echinoideorum	82.2818	854	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_003415655.1	s__Vibrio maerlii	80.9326	431	1653	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 12:41:47,476] [INFO] GTDB search result was written to GCF_024347575.1_ASM2434757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:47,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:47,480] [INFO] DFAST_QC result json was written to GCF_024347575.1_ASM2434757v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:47,481] [INFO] DFAST_QC completed!
[2024-01-24 12:41:47,481] [INFO] Total running time: 0h1m27s