[2024-01-24 12:13:56,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:56,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:56,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference
[2024-01-24 12:13:58,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:58,311] [INFO] Task started: Prodigal
[2024-01-24 12:13:58,312] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f37190c-0f43-47b2-8c20-ba66f27dd9d3/GCF_009931115.1_ASM993111v1_genomic.fna.gz | prodigal -d GCF_009931115.1_ASM993111v1_genomic.fna/cds.fna -a GCF_009931115.1_ASM993111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:12,051] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:12,051] [INFO] Task started: HMMsearch
[2024-01-24 12:14:12,051] [INFO] Running command: hmmsearch --tblout GCF_009931115.1_ASM993111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference/reference_markers.hmm GCF_009931115.1_ASM993111v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:12,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:12,414] [INFO] Found 6/6 markers.
[2024-01-24 12:14:12,462] [INFO] Query marker FASTA was written to GCF_009931115.1_ASM993111v1_genomic.fna/markers.fasta
[2024-01-24 12:14:12,463] [INFO] Task started: Blastn
[2024-01-24 12:14:12,463] [INFO] Running command: blastn -query GCF_009931115.1_ASM993111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference/reference_markers.fasta -out GCF_009931115.1_ASM993111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:13,353] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:13,358] [INFO] Selected 11 target genomes.
[2024-01-24 12:14:13,358] [INFO] Target genome list was writen to GCF_009931115.1_ASM993111v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:13,364] [INFO] Task started: fastANI
[2024-01-24 12:14:13,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f37190c-0f43-47b2-8c20-ba66f27dd9d3/GCF_009931115.1_ASM993111v1_genomic.fna.gz --refList GCF_009931115.1_ASM993111v1_genomic.fna/target_genomes.txt --output GCF_009931115.1_ASM993111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:23,447] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:23,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:23,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:23,457] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:23,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:23,457] [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 hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	100.0	1400	1403	95	conclusive
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	99.9884	1385	1403	95	conclusive
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	82.5183	822	1403	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	81.7376	747	1403	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	81.6276	726	1403	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	81.3232	789	1403	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	81.2385	723	1403	95	below_threshold
Microbulbifer aggregans	strain=CCB-MM1	GCA_001750105.1	1769779	1769779	type	True	79.516	458	1403	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	79.4008	521	1403	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.0474	121	1403	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.6333	113	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:23,459] [INFO] DFAST Taxonomy check result was written to GCF_009931115.1_ASM993111v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:23,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:23,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:23,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference/checkm_data
[2024-01-24 12:14:23,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:23,511] [INFO] Task started: CheckM
[2024-01-24 12:14:23,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009931115.1_ASM993111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009931115.1_ASM993111v1_genomic.fna/checkm_input GCF_009931115.1_ASM993111v1_genomic.fna/checkm_result
[2024-01-24 12:15:06,722] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:06,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,747] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:06,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:06,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009931115.1_ASM993111v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:06,748] [INFO] Task started: Blastn
[2024-01-24 12:15:06,748] [INFO] Running command: blastn -query GCF_009931115.1_ASM993111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3de9d5ff-cfb1-4cca-8588-43b5958a0c32/dqc_reference/reference_markers_gtdb.fasta -out GCF_009931115.1_ASM993111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:08,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:08,252] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:08,252] [INFO] Target genome list was writen to GCF_009931115.1_ASM993111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:08,260] [INFO] Task started: fastANI
[2024-01-24 12:15:08,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f37190c-0f43-47b2-8c20-ba66f27dd9d3/GCF_009931115.1_ASM993111v1_genomic.fna.gz --refList GCF_009931115.1_ASM993111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009931115.1_ASM993111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:17,295] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:17,312] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:17,312] [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_009931115.1	s__Microbulbifer hydrolyticus	100.0	1400	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013367775.1	s__Microbulbifer sp013367775	83.2169	939	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303155.1	s__Microbulbifer salipaludis	82.6125	816	1403	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	82.5375	849	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002009015.1	s__Microbulbifer mangrovi	82.4897	825	1403	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	81.9997	825	1403	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	81.7641	732	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771435.1	s__Microbulbifer harenosus	81.3211	790	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
GCF_001999945.1	s__Microbulbifer agarilyticus_A	80.8119	673	1403	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 12:15:17,315] [INFO] GTDB search result was written to GCF_009931115.1_ASM993111v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:17,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:17,319] [INFO] DFAST_QC result json was written to GCF_009931115.1_ASM993111v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:17,319] [INFO] DFAST_QC completed!
[2024-01-24 12:15:17,319] [INFO] Total running time: 0h1m20s