[2024-01-24 12:23:50,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,969] [INFO] DQC Reference Directory: /var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference
[2024-01-24 12:23:52,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,233] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,233] [INFO] Running command: gunzip -c /var/lib/cwl/stg09e3bcfc-5d6c-442f-9a83-e6977cb74b4f/GCF_002009015.1_ASM200901v1_genomic.fna.gz | prodigal -d GCF_002009015.1_ASM200901v1_genomic.fna/cds.fna -a GCF_002009015.1_ASM200901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:04,303] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:04,303] [INFO] Task started: HMMsearch
[2024-01-24 12:24:04,304] [INFO] Running command: hmmsearch --tblout GCF_002009015.1_ASM200901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference/reference_markers.hmm GCF_002009015.1_ASM200901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:04,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:04,593] [INFO] Found 6/6 markers.
[2024-01-24 12:24:04,633] [INFO] Query marker FASTA was written to GCF_002009015.1_ASM200901v1_genomic.fna/markers.fasta
[2024-01-24 12:24:04,634] [INFO] Task started: Blastn
[2024-01-24 12:24:04,634] [INFO] Running command: blastn -query GCF_002009015.1_ASM200901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference/reference_markers.fasta -out GCF_002009015.1_ASM200901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:05,427] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:05,432] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:05,432] [INFO] Target genome list was writen to GCF_002009015.1_ASM200901v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:05,435] [INFO] Task started: fastANI
[2024-01-24 12:24:05,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e3bcfc-5d6c-442f-9a83-e6977cb74b4f/GCF_002009015.1_ASM200901v1_genomic.fna.gz --refList GCF_002009015.1_ASM200901v1_genomic.fna/target_genomes.txt --output GCF_002009015.1_ASM200901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:14,469] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:14,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:14,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:14,479] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:14,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:14,479] [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
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	100.0	1340	1356	95	conclusive
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	82.4609	819	1356	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	82.4155	823	1356	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	81.1409	695	1356	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	81.1316	705	1356	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	80.8185	745	1356	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	80.5169	669	1356	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	79.0791	505	1356	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	78.9382	514	1356	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.8821	113	1356	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.8401	102	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:14,481] [INFO] DFAST Taxonomy check result was written to GCF_002009015.1_ASM200901v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:14,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:14,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:14,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference/checkm_data
[2024-01-24 12:24:14,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:14,531] [INFO] Task started: CheckM
[2024-01-24 12:24:14,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002009015.1_ASM200901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002009015.1_ASM200901v1_genomic.fna/checkm_input GCF_002009015.1_ASM200901v1_genomic.fna/checkm_result
[2024-01-24 12:24:52,981] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:52,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:53,005] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:53,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:53,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002009015.1_ASM200901v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:53,006] [INFO] Task started: Blastn
[2024-01-24 12:24:53,006] [INFO] Running command: blastn -query GCF_002009015.1_ASM200901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabb9cd26-8aa4-4ff7-8821-ceee0b30c810/dqc_reference/reference_markers_gtdb.fasta -out GCF_002009015.1_ASM200901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:54,367] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:54,371] [INFO] Selected 9 target genomes.
[2024-01-24 12:24:54,371] [INFO] Target genome list was writen to GCF_002009015.1_ASM200901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:54,377] [INFO] Task started: fastANI
[2024-01-24 12:24:54,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e3bcfc-5d6c-442f-9a83-e6977cb74b4f/GCF_002009015.1_ASM200901v1_genomic.fna.gz --refList GCF_002009015.1_ASM200901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002009015.1_ASM200901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:02,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:02,465] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:02,465] [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_002009015.1	s__Microbulbifer mangrovi	100.0	1340	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013367775.1	s__Microbulbifer sp013367775	89.2993	1121	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931115.1	s__Microbulbifer hydrolyticus	82.4251	822	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017303155.1	s__Microbulbifer salipaludis	81.9595	796	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639145.1	s__Microbulbifer sp001639145	81.9382	797	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	81.8265	847	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708675.1	s__Microbulbifer sp000708675	81.3442	698	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002959965.1	s__Microbulbifer pacificus	80.9557	706	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999945.1	s__Microbulbifer agarilyticus_A	80.3808	627	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:02,467] [INFO] GTDB search result was written to GCF_002009015.1_ASM200901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:02,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:02,471] [INFO] DFAST_QC result json was written to GCF_002009015.1_ASM200901v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:02,471] [INFO] DFAST_QC completed!
[2024-01-24 12:25:02,471] [INFO] Total running time: 0h1m12s