[2024-01-24 12:06:14,061] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference
[2024-01-24 12:06:15,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,606] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d9642d6-a8e0-4871-a9f7-d989c047585c/GCF_005281815.1_ASM528181v1_genomic.fna.gz | prodigal -d GCF_005281815.1_ASM528181v1_genomic.fna/cds.fna -a GCF_005281815.1_ASM528181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:28,022] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:28,022] [INFO] Task started: HMMsearch
[2024-01-24 12:06:28,022] [INFO] Running command: hmmsearch --tblout GCF_005281815.1_ASM528181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference/reference_markers.hmm GCF_005281815.1_ASM528181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,397] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,465] [INFO] Query marker FASTA was written to GCF_005281815.1_ASM528181v1_genomic.fna/markers.fasta
[2024-01-24 12:06:28,466] [INFO] Task started: Blastn
[2024-01-24 12:06:28,466] [INFO] Running command: blastn -query GCF_005281815.1_ASM528181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference/reference_markers.fasta -out GCF_005281815.1_ASM528181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,274] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,283] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:29,283] [INFO] Target genome list was writen to GCF_005281815.1_ASM528181v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,293] [INFO] Task started: fastANI
[2024-01-24 12:06:29,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d9642d6-a8e0-4871-a9f7-d989c047585c/GCF_005281815.1_ASM528181v1_genomic.fna.gz --refList GCF_005281815.1_ASM528181v1_genomic.fna/target_genomes.txt --output GCF_005281815.1_ASM528181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:48,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:48,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:48,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:48,983] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:48,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:48,984] [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 chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	100.0	1689	1697	95	conclusive
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	99.9954	1694	1697	95	conclusive
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	99.9931	1686	1697	95	conclusive
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	88.7044	1272	1697	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	88.6788	1251	1697	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	88.5712	1282	1697	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	87.9225	1258	1697	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	87.9117	1250	1697	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	87.4925	1187	1697	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	87.3869	1197	1697	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	86.3582	1120	1697	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	83.5058	860	1697	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	83.2759	853	1697	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	82.7691	662	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:48,986] [INFO] DFAST Taxonomy check result was written to GCF_005281815.1_ASM528181v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:48,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:48,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:48,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference/checkm_data
[2024-01-24 12:06:48,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:49,041] [INFO] Task started: CheckM
[2024-01-24 12:06:49,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005281815.1_ASM528181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005281815.1_ASM528181v1_genomic.fna/checkm_input GCF_005281815.1_ASM528181v1_genomic.fna/checkm_result
[2024-01-24 12:07:30,158] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:30,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:30,187] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:30,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:30,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005281815.1_ASM528181v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:30,188] [INFO] Task started: Blastn
[2024-01-24 12:07:30,188] [INFO] Running command: blastn -query GCF_005281815.1_ASM528181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c3aa2c1-b990-4103-b2c2-fc480e775eda/dqc_reference/reference_markers_gtdb.fasta -out GCF_005281815.1_ASM528181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:31,155] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:31,158] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:31,158] [INFO] Target genome list was writen to GCF_005281815.1_ASM528181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:31,169] [INFO] Task started: fastANI
[2024-01-24 12:07:31,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d9642d6-a8e0-4871-a9f7-d989c047585c/GCF_005281815.1_ASM528181v1_genomic.fna.gz --refList GCF_005281815.1_ASM528181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005281815.1_ASM528181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:47,297] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:47,313] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:47,314] [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_005281815.1	s__Vibrio chagasii	100.0	1689	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	conclusive
GCF_002954585.1	s__Vibrio chagasii_A	94.8815	1455	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCA_000169995.1	s__Vibrio sp000169995	94.8573	1350	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635455.1	s__Vibrio sp001635455	93.7068	1393	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156475.1	s__Vibrio gigantis	88.6788	1251	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_013394185.1	s__Vibrio sp013394185	88.6556	1276	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	88.2071	1178	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272045.2	s__Vibrio crassostreae_C	87.7534	1217	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_001557875.1	s__Vibrio splendidus_F	87.7327	1236	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_002875705.1	s__Vibrio sp002875705	87.6379	1179	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_000695685.1	s__Vibrio fortis	83.4402	892	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_005281835.1	s__Vibrio profundi	82.7814	661	1697	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 12:07:47,315] [INFO] GTDB search result was written to GCF_005281815.1_ASM528181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:47,316] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:47,320] [INFO] DFAST_QC result json was written to GCF_005281815.1_ASM528181v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:47,320] [INFO] DFAST_QC completed!
[2024-01-24 12:07:47,320] [INFO] Total running time: 0h1m33s