[2024-01-24 13:49:33,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference
[2024-01-24 13:49:34,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,821] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg37ec6632-ea94-4ea3-862f-7e157a55795b/GCF_002157735.2_ASM215773v2_genomic.fna.gz | prodigal -d GCF_002157735.2_ASM215773v2_genomic.fna/cds.fna -a GCF_002157735.2_ASM215773v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,743] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,743] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,743] [INFO] Running command: hmmsearch --tblout GCF_002157735.2_ASM215773v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference/reference_markers.hmm GCF_002157735.2_ASM215773v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,035] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,036] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,086] [INFO] Query marker FASTA was written to GCF_002157735.2_ASM215773v2_genomic.fna/markers.fasta
[2024-01-24 13:49:43,086] [INFO] Task started: Blastn
[2024-01-24 13:49:43,086] [INFO] Running command: blastn -query GCF_002157735.2_ASM215773v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference/reference_markers.fasta -out GCF_002157735.2_ASM215773v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,949] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,955] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:43,956] [INFO] Target genome list was writen to GCF_002157735.2_ASM215773v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,960] [INFO] Task started: fastANI
[2024-01-24 13:49:43,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ec6632-ea94-4ea3-862f-7e157a55795b/GCF_002157735.2_ASM215773v2_genomic.fna.gz --refList GCF_002157735.2_ASM215773v2_genomic.fna/target_genomes.txt --output GCF_002157735.2_ASM215773v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:54,211] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:54,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:54,227] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:54,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:54,227] [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 aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	100.0	1124	1124	95	conclusive
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	81.5442	663	1124	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	81.3829	618	1124	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	80.823	605	1124	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	80.7568	580	1124	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	79.9979	502	1124	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.7814	199	1124	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.6304	204	1124	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.4873	423	1124	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	79.484	177	1124	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.2862	208	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,229] [INFO] DFAST Taxonomy check result was written to GCF_002157735.2_ASM215773v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:54,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:54,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:54,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference/checkm_data
[2024-01-24 13:49:54,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:54,267] [INFO] Task started: CheckM
[2024-01-24 13:49:54,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002157735.2_ASM215773v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002157735.2_ASM215773v2_genomic.fna/checkm_input GCF_002157735.2_ASM215773v2_genomic.fna/checkm_result
[2024-01-24 13:50:25,603] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:25,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:25,622] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:25,622] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:25,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002157735.2_ASM215773v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:25,623] [INFO] Task started: Blastn
[2024-01-24 13:50:25,623] [INFO] Running command: blastn -query GCF_002157735.2_ASM215773v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5375f2c8-c5fb-4d03-804c-ec286664c6a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002157735.2_ASM215773v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:26,916] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:26,920] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:26,920] [INFO] Target genome list was writen to GCF_002157735.2_ASM215773v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:26,926] [INFO] Task started: fastANI
[2024-01-24 13:50:26,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ec6632-ea94-4ea3-862f-7e157a55795b/GCF_002157735.2_ASM215773v2_genomic.fna.gz --refList GCF_002157735.2_ASM215773v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002157735.2_ASM215773v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:34,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:34,253] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:34,253] [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_002157735.2	s__Vibrio aphrogenes	100.0	1124	1124	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_002934045.1	s__Vibrio gangliei	81.5153	665	1124	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	81.3322	616	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_002218045.2	s__Vibrio rumoiensis	80.8436	606	1124	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	80.7356	580	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002218025.2	s__Vibrio casei	80.0146	500	1124	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	79.9532	502	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694375.1	s__Vibrio sp014694375	79.069	421	1124	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 13:50:34,256] [INFO] GTDB search result was written to GCF_002157735.2_ASM215773v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:34,257] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:34,262] [INFO] DFAST_QC result json was written to GCF_002157735.2_ASM215773v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:34,262] [INFO] DFAST_QC completed!
[2024-01-24 13:50:34,263] [INFO] Total running time: 0h1m1s