[2024-01-24 13:12:56,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference
[2024-01-24 13:12:57,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,361] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg43b550d5-bc20-47a6-ba5c-61e4a2d99d89/GCF_009938205.1_ASM993820v1_genomic.fna.gz | prodigal -d GCF_009938205.1_ASM993820v1_genomic.fna/cds.fna -a GCF_009938205.1_ASM993820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:10,828] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:10,828] [INFO] Task started: HMMsearch
[2024-01-24 13:13:10,829] [INFO] Running command: hmmsearch --tblout GCF_009938205.1_ASM993820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference/reference_markers.hmm GCF_009938205.1_ASM993820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:11,134] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:11,136] [INFO] Found 6/6 markers.
[2024-01-24 13:13:11,181] [INFO] Query marker FASTA was written to GCF_009938205.1_ASM993820v1_genomic.fna/markers.fasta
[2024-01-24 13:13:11,181] [INFO] Task started: Blastn
[2024-01-24 13:13:11,181] [INFO] Running command: blastn -query GCF_009938205.1_ASM993820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference/reference_markers.fasta -out GCF_009938205.1_ASM993820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:12,066] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:12,072] [INFO] Selected 12 target genomes.
[2024-01-24 13:13:12,073] [INFO] Target genome list was writen to GCF_009938205.1_ASM993820v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:12,078] [INFO] Task started: fastANI
[2024-01-24 13:13:12,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b550d5-bc20-47a6-ba5c-61e4a2d99d89/GCF_009938205.1_ASM993820v1_genomic.fna.gz --refList GCF_009938205.1_ASM993820v1_genomic.fna/target_genomes.txt --output GCF_009938205.1_ASM993820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:26,222] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:26,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:26,234] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:26,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:26,235] [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 panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	100.0	1617	1617	95	conclusive
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	99.9907	1598	1617	95	conclusive
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	83.816	909	1617	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	83.3653	907	1617	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	81.522	816	1617	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.7523	387	1617	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	80.641	621	1617	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	80.5056	561	1617	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	80.4295	411	1617	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	80.1767	370	1617	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.1493	474	1617	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.9814	331	1617	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,237] [INFO] DFAST Taxonomy check result was written to GCF_009938205.1_ASM993820v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:26,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:26,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:26,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference/checkm_data
[2024-01-24 13:13:26,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:26,295] [INFO] Task started: CheckM
[2024-01-24 13:13:26,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009938205.1_ASM993820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009938205.1_ASM993820v1_genomic.fna/checkm_input GCF_009938205.1_ASM993820v1_genomic.fna/checkm_result
[2024-01-24 13:14:09,861] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:09,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:09,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:09,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009938205.1_ASM993820v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:09,888] [INFO] Task started: Blastn
[2024-01-24 13:14:09,888] [INFO] Running command: blastn -query GCF_009938205.1_ASM993820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed4fb94-e2ad-48aa-a457-d69db2b766dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_009938205.1_ASM993820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:11,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:11,119] [INFO] Selected 9 target genomes.
[2024-01-24 13:14:11,119] [INFO] Target genome list was writen to GCF_009938205.1_ASM993820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:11,127] [INFO] Task started: fastANI
[2024-01-24 13:14:11,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b550d5-bc20-47a6-ba5c-61e4a2d99d89/GCF_009938205.1_ASM993820v1_genomic.fna.gz --refList GCF_009938205.1_ASM993820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009938205.1_ASM993820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:20,705] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:20,717] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:20,718] [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_009938205.1	s__Vibrio panuliri	100.0	1617	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	conclusive
GCF_009938225.1	s__Vibrio ponticus	83.8014	909	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_003350325.1	s__Vibrio rhodolitus	83.3653	907	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_015278125.1	s__Vibrio sp015278125	83.263	895	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938165.1	s__Vibrio taketomensis	81.9492	733	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_014050145.1	s__Vibrio marinisediminis	81.522	816	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	80.6486	619	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_002741985.1	s__Vibrio rotiferianus	80.4266	412	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_004551525.1	s__Vibrio ouci	80.3007	443	1617	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 13:14:20,719] [INFO] GTDB search result was written to GCF_009938205.1_ASM993820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:20,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:20,727] [INFO] DFAST_QC result json was written to GCF_009938205.1_ASM993820v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:20,727] [INFO] DFAST_QC completed!
[2024-01-24 13:14:20,727] [INFO] Total running time: 0h1m25s