[2024-01-24 13:13:10,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:10,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:10,889] [INFO] DQC Reference Directory: /var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference
[2024-01-24 13:13:12,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:12,188] [INFO] Task started: Prodigal
[2024-01-24 13:13:12,189] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd7a0701-7dea-4735-a95e-20a91d8269d3/GCF_001562055.1_ASM156205v1_genomic.fna.gz | prodigal -d GCF_001562055.1_ASM156205v1_genomic.fna/cds.fna -a GCF_001562055.1_ASM156205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:22,908] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:22,909] [INFO] Task started: HMMsearch
[2024-01-24 13:13:22,909] [INFO] Running command: hmmsearch --tblout GCF_001562055.1_ASM156205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference/reference_markers.hmm GCF_001562055.1_ASM156205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:23,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:23,192] [INFO] Found 6/6 markers.
[2024-01-24 13:13:23,244] [INFO] Query marker FASTA was written to GCF_001562055.1_ASM156205v1_genomic.fna/markers.fasta
[2024-01-24 13:13:23,244] [INFO] Task started: Blastn
[2024-01-24 13:13:23,244] [INFO] Running command: blastn -query GCF_001562055.1_ASM156205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference/reference_markers.fasta -out GCF_001562055.1_ASM156205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:23,982] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:23,985] [INFO] Selected 20 target genomes.
[2024-01-24 13:13:23,986] [INFO] Target genome list was writen to GCF_001562055.1_ASM156205v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:24,106] [INFO] Task started: fastANI
[2024-01-24 13:13:24,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd7a0701-7dea-4735-a95e-20a91d8269d3/GCF_001562055.1_ASM156205v1_genomic.fna.gz --refList GCF_001562055.1_ASM156205v1_genomic.fna/target_genomes.txt --output GCF_001562055.1_ASM156205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:38,288] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:38,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:38,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:38,296] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:38,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:38,296] [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
Pseudovibrio stylochi	strain=UST20140214-052	GCA_001562055.1	1807766	1807766	type	True	100.0	1206	1206	95	conclusive
Pseudovibrio hongkongensis	strain=UST20140214-015B	GCA_001561995.1	1647556	1647556	type	True	80.8015	253	1206	95	below_threshold
Pseudovibrio denitrificans	strain=DSM 17465	GCA_900116575.1	258256	258256	type	True	78.099	132	1206	95	below_threshold
Pseudovibrio japonicus	strain=KCTC 12861	GCA_014651595.1	366534	366534	type	True	77.8003	128	1206	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_018282095.1	1898042	1898042	type	True	77.7171	140	1206	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_001941685.1	1898042	1898042	type	True	77.6929	142	1206	95	below_threshold
Pseudovibrio ascidiaceicola	strain=DSM 16392	GCA_900114245.1	285279	285279	type	True	77.4731	137	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,298] [INFO] DFAST Taxonomy check result was written to GCF_001562055.1_ASM156205v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:38,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:38,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:38,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference/checkm_data
[2024-01-24 13:13:38,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:38,337] [INFO] Task started: CheckM
[2024-01-24 13:13:38,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001562055.1_ASM156205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001562055.1_ASM156205v1_genomic.fna/checkm_input GCF_001562055.1_ASM156205v1_genomic.fna/checkm_result
[2024-01-24 13:14:13,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:13,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,395] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:13,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:13,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001562055.1_ASM156205v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:13,397] [INFO] Task started: Blastn
[2024-01-24 13:14:13,397] [INFO] Running command: blastn -query GCF_001562055.1_ASM156205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7188d10-1cce-4edf-a8df-9d0aeb6cb3bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001562055.1_ASM156205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:14,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:14,510] [INFO] Selected 18 target genomes.
[2024-01-24 13:14:14,510] [INFO] Target genome list was writen to GCF_001562055.1_ASM156205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:14,543] [INFO] Task started: fastANI
[2024-01-24 13:14:14,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd7a0701-7dea-4735-a95e-20a91d8269d3/GCF_001562055.1_ASM156205v1_genomic.fna.gz --refList GCF_001562055.1_ASM156205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001562055.1_ASM156205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:27,640] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:27,652] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:27,653] [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_001562055.1	s__Pseudovibrio stylochi	100.0	1206	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001561995.1	s__Pseudovibrio hongkongensis	80.7926	254	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651595.1	s__Pseudovibrio japonicus	77.8174	129	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018282095.1	s__Pseudovibrio brasiliensis	77.6956	141	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900143565.1	s__Pseudovibrio sp900143565	77.5704	130	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.56	96.48	0.91	0.89	8	-
GCF_900110875.1	s__Pseudovibrio axinellae	77.5524	113	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900114245.1	s__Pseudovibrio ascidiaceicola	77.443	137	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.13	95.42	0.93	0.92	3	-
GCF_001623075.1	s__Pseudovibrio sp001623075	77.3615	128	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.77	96.77	0.91	0.91	2	-
GCF_900104145.1	s__Pseudovibrio sp900104145	77.0687	119	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:27,654] [INFO] GTDB search result was written to GCF_001562055.1_ASM156205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:27,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:27,658] [INFO] DFAST_QC result json was written to GCF_001562055.1_ASM156205v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:27,658] [INFO] DFAST_QC completed!
[2024-01-24 13:14:27,658] [INFO] Total running time: 0h1m17s