[2024-01-24 13:37:25,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference
[2024-01-24 13:37:26,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:26,539] [INFO] Task started: Prodigal
[2024-01-24 13:37:26,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a5ee8ac-c589-4e34-a803-745965427b98/GCF_022554105.1_ASM2255410v1_genomic.fna.gz | prodigal -d GCF_022554105.1_ASM2255410v1_genomic.fna/cds.fna -a GCF_022554105.1_ASM2255410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:38,807] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:38,807] [INFO] Task started: HMMsearch
[2024-01-24 13:37:38,807] [INFO] Running command: hmmsearch --tblout GCF_022554105.1_ASM2255410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference/reference_markers.hmm GCF_022554105.1_ASM2255410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:39,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:39,132] [INFO] Found 6/6 markers.
[2024-01-24 13:37:39,166] [INFO] Query marker FASTA was written to GCF_022554105.1_ASM2255410v1_genomic.fna/markers.fasta
[2024-01-24 13:37:39,166] [INFO] Task started: Blastn
[2024-01-24 13:37:39,166] [INFO] Running command: blastn -query GCF_022554105.1_ASM2255410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference/reference_markers.fasta -out GCF_022554105.1_ASM2255410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:40,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:40,020] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:40,021] [INFO] Target genome list was writen to GCF_022554105.1_ASM2255410v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:40,041] [INFO] Task started: fastANI
[2024-01-24 13:37:40,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5ee8ac-c589-4e34-a803-745965427b98/GCF_022554105.1_ASM2255410v1_genomic.fna.gz --refList GCF_022554105.1_ASM2255410v1_genomic.fna/target_genomes.txt --output GCF_022554105.1_ASM2255410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:50,691] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:50,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:50,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:50,712] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:50,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:50,712] [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 elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	100.0	1352	1354	95	conclusive
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	99.9968	1353	1354	95	conclusive
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	81.6216	745	1354	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	81.5662	739	1354	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	81.3402	766	1354	95	below_threshold
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	81.171	709	1354	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	81.0503	694	1354	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	79.43	520	1354	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	79.0097	403	1354	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.7971	90	1354	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.7961	86	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,715] [INFO] DFAST Taxonomy check result was written to GCF_022554105.1_ASM2255410v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:50,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:50,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:50,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference/checkm_data
[2024-01-24 13:37:50,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:50,761] [INFO] Task started: CheckM
[2024-01-24 13:37:50,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022554105.1_ASM2255410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022554105.1_ASM2255410v1_genomic.fna/checkm_input GCF_022554105.1_ASM2255410v1_genomic.fna/checkm_result
[2024-01-24 13:38:29,965] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:29,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:29,989] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:29,989] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:29,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022554105.1_ASM2255410v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:29,990] [INFO] Task started: Blastn
[2024-01-24 13:38:29,990] [INFO] Running command: blastn -query GCF_022554105.1_ASM2255410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f5cdab9-a1f2-41f8-9b2e-bcfb7193a628/dqc_reference/reference_markers_gtdb.fasta -out GCF_022554105.1_ASM2255410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:31,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:31,423] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:31,423] [INFO] Target genome list was writen to GCF_022554105.1_ASM2255410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:31,436] [INFO] Task started: fastANI
[2024-01-24 13:38:31,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5ee8ac-c589-4e34-a803-745965427b98/GCF_022554105.1_ASM2255410v1_genomic.fna.gz --refList GCF_022554105.1_ASM2255410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022554105.1_ASM2255410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:42,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:42,460] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:42,461] [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_000708675.1	s__Microbulbifer sp000708675	87.4276	1152	1354	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	82.0529	776	1354	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	82.0039	752	1354	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	81.9599	769	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013367775.1	s__Microbulbifer sp013367775	81.8857	785	1354	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	81.5848	737	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002959965.1	s__Microbulbifer pacificus	81.5223	738	1354	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	81.3677	722	1354	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	81.2888	772	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
GCF_002009015.1	s__Microbulbifer mangrovi	81.1582	711	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	79.4349	518	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100355.1	s__Microbulbifer yueqingensis	79.0147	402	1354	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 13:38:42,462] [INFO] GTDB search result was written to GCF_022554105.1_ASM2255410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:42,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:42,466] [INFO] DFAST_QC result json was written to GCF_022554105.1_ASM2255410v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:42,466] [INFO] DFAST_QC completed!
[2024-01-24 13:38:42,466] [INFO] Total running time: 0h1m17s