[2024-01-24 13:17:05,509] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference
[2024-01-24 13:17:06,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,934] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg81bf690c-3618-4cda-9695-d02f36e08f3d/GCF_002934045.1_ASM293404v1_genomic.fna.gz | prodigal -d GCF_002934045.1_ASM293404v1_genomic.fna/cds.fna -a GCF_002934045.1_ASM293404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:15,582] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:15,582] [INFO] Task started: HMMsearch
[2024-01-24 13:17:15,583] [INFO] Running command: hmmsearch --tblout GCF_002934045.1_ASM293404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference/reference_markers.hmm GCF_002934045.1_ASM293404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:15,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:15,886] [INFO] Found 6/6 markers.
[2024-01-24 13:17:15,925] [INFO] Query marker FASTA was written to GCF_002934045.1_ASM293404v1_genomic.fna/markers.fasta
[2024-01-24 13:17:15,926] [INFO] Task started: Blastn
[2024-01-24 13:17:15,926] [INFO] Running command: blastn -query GCF_002934045.1_ASM293404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference/reference_markers.fasta -out GCF_002934045.1_ASM293404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:16,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:16,812] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:16,813] [INFO] Target genome list was writen to GCF_002934045.1_ASM293404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:16,817] [INFO] Task started: fastANI
[2024-01-24 13:17:16,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg81bf690c-3618-4cda-9695-d02f36e08f3d/GCF_002934045.1_ASM293404v1_genomic.fna.gz --refList GCF_002934045.1_ASM293404v1_genomic.fna/target_genomes.txt --output GCF_002934045.1_ASM293404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:28,928] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:28,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:28,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:28,941] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:28,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:28,941] [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 gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	100.0	1175	1179	95	conclusive
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	81.5919	651	1179	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	81.309	645	1179	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	81.2439	648	1179	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	80.9705	656	1179	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	80.2169	518	1179	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.4373	405	1179	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.0226	228	1179	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.0221	221	1179	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.003	208	1179	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.6579	217	1179	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.622	215	1179	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	78.5635	215	1179	95	below_threshold
Aliivibrio finisterrensis	strain=LMG 23869	GCA_008933155.1	511998	511998	suspected-type	True	78.5073	186	1179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:28,949] [INFO] DFAST Taxonomy check result was written to GCF_002934045.1_ASM293404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:28,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:28,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:28,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference/checkm_data
[2024-01-24 13:17:28,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:28,994] [INFO] Task started: CheckM
[2024-01-24 13:17:28,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934045.1_ASM293404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934045.1_ASM293404v1_genomic.fna/checkm_input GCF_002934045.1_ASM293404v1_genomic.fna/checkm_result
[2024-01-24 13:18:01,419] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:01,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:01,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:01,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934045.1_ASM293404v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:01,445] [INFO] Task started: Blastn
[2024-01-24 13:18:01,445] [INFO] Running command: blastn -query GCF_002934045.1_ASM293404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e4fcc50-d7e7-4588-ad21-d48b6188d477/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934045.1_ASM293404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:02,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:02,717] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:02,718] [INFO] Target genome list was writen to GCF_002934045.1_ASM293404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:02,730] [INFO] Task started: fastANI
[2024-01-24 13:18:02,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg81bf690c-3618-4cda-9695-d02f36e08f3d/GCF_002934045.1_ASM293404v1_genomic.fna.gz --refList GCF_002934045.1_ASM293404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934045.1_ASM293404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:11,342] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:11,354] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:11,354] [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_002934045.1	s__Vibrio gangliei	100.0	1175	1179	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_002157735.2	s__Vibrio aphrogenes	81.5657	653	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218005.2	s__Vibrio algivorus	81.3227	641	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_000426765.1	s__Vibrio litoralis	81.2261	648	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002218045.2	s__Vibrio rumoiensis	80.9738	656	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218025.2	s__Vibrio casei	80.1982	520	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_000286955.2	s__Vibrio rumoiensis_A	79.8508	496	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601765.2	s__Vibrio sp009601765	79.4243	406	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.01	99.01	0.85	0.85	2	-
GCF_000827885.1	s__Vibrio renipiscarius	78.6585	216	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008933155.1	s__Aliivibrio finisterrensis	78.5073	186	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	95.53	95.03	0.81	0.80	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:11,356] [INFO] GTDB search result was written to GCF_002934045.1_ASM293404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:11,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:11,360] [INFO] DFAST_QC result json was written to GCF_002934045.1_ASM293404v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:11,360] [INFO] DFAST_QC completed!
[2024-01-24 13:18:11,360] [INFO] Total running time: 0h1m6s