[2024-01-24 11:13:49,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference
[2024-01-24 11:13:50,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,639] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,639] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb86009f-7ac6-4dc0-95c7-97db239e9dab/GCF_015223435.1_ASM1522343v1_genomic.fna.gz | prodigal -d GCF_015223435.1_ASM1522343v1_genomic.fna/cds.fna -a GCF_015223435.1_ASM1522343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:57,598] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:57,599] [INFO] Task started: HMMsearch
[2024-01-24 11:13:57,599] [INFO] Running command: hmmsearch --tblout GCF_015223435.1_ASM1522343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference/reference_markers.hmm GCF_015223435.1_ASM1522343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:57,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:57,861] [INFO] Found 6/6 markers.
[2024-01-24 11:13:57,889] [INFO] Query marker FASTA was written to GCF_015223435.1_ASM1522343v1_genomic.fna/markers.fasta
[2024-01-24 11:13:57,890] [INFO] Task started: Blastn
[2024-01-24 11:13:57,890] [INFO] Running command: blastn -query GCF_015223435.1_ASM1522343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference/reference_markers.fasta -out GCF_015223435.1_ASM1522343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:58,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:58,665] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:58,665] [INFO] Target genome list was writen to GCF_015223435.1_ASM1522343v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:58,671] [INFO] Task started: fastANI
[2024-01-24 11:13:58,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb86009f-7ac6-4dc0-95c7-97db239e9dab/GCF_015223435.1_ASM1522343v1_genomic.fna.gz --refList GCF_015223435.1_ASM1522343v1_genomic.fna/target_genomes.txt --output GCF_015223435.1_ASM1522343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:09,135] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:09,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:09,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:09,151] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:09,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:09,152] [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 hibernica	strain=B1.19	GCA_015223435.1	2587465	2587465	type	True	100.0	1069	1073	95	conclusive
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	81.4388	473	1073	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	80.8011	584	1073	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	79.8251	447	1073	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	79.7206	418	1073	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	79.5976	425	1073	95	below_threshold
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	79.3185	368	1073	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	79.248	392	1073	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	78.6572	167	1073	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.4455	150	1073	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.4357	152	1073	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	78.3533	157	1073	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.2164	150	1073	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	78.0586	163	1073	95	below_threshold
Aliivibrio fischeri	strain=ATCC 7744	GCA_016464335.1	668	668	suspected-type	True	77.943	190	1073	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:09,154] [INFO] DFAST Taxonomy check result was written to GCF_015223435.1_ASM1522343v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:09,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:09,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:09,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference/checkm_data
[2024-01-24 11:14:09,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:09,190] [INFO] Task started: CheckM
[2024-01-24 11:14:09,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015223435.1_ASM1522343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015223435.1_ASM1522343v1_genomic.fna/checkm_input GCF_015223435.1_ASM1522343v1_genomic.fna/checkm_result
[2024-01-24 11:14:36,122] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:36,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:36,142] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:36,142] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:36,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015223435.1_ASM1522343v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:36,143] [INFO] Task started: Blastn
[2024-01-24 11:14:36,143] [INFO] Running command: blastn -query GCF_015223435.1_ASM1522343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57c15770-38f5-424e-8b11-01af535445f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_015223435.1_ASM1522343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:37,368] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:37,371] [INFO] Selected 9 target genomes.
[2024-01-24 11:14:37,372] [INFO] Target genome list was writen to GCF_015223435.1_ASM1522343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:37,379] [INFO] Task started: fastANI
[2024-01-24 11:14:37,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb86009f-7ac6-4dc0-95c7-97db239e9dab/GCF_015223435.1_ASM1522343v1_genomic.fna.gz --refList GCF_015223435.1_ASM1522343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015223435.1_ASM1522343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:44,369] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:44,384] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:44,384] [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_015223435.1	s__Vibrio hibernica	100.0	1069	1073	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_014694375.1	s__Vibrio sp014694375	91.7826	882	1073	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	81.4388	473	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_009601765.2	s__Vibrio sp009601765	80.7999	585	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.01	99.01	0.85	0.85	2	-
GCF_002218045.2	s__Vibrio rumoiensis	79.8132	448	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286955.2	s__Vibrio rumoiensis_A	79.7691	433	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426765.1	s__Vibrio litoralis	79.7248	417	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002157735.2	s__Vibrio aphrogenes	79.3185	368	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934045.1	s__Vibrio gangliei	79.2359	393	1073	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 11:14:44,385] [INFO] GTDB search result was written to GCF_015223435.1_ASM1522343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:44,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:44,389] [INFO] DFAST_QC result json was written to GCF_015223435.1_ASM1522343v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:44,389] [INFO] DFAST_QC completed!
[2024-01-24 11:14:44,389] [INFO] Total running time: 0h0m55s