[2024-01-24 12:47:27,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:27,918] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:27,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference
[2024-01-24 12:47:29,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:29,260] [INFO] Task started: Prodigal
[2024-01-24 12:47:29,261] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7dc837a-fa14-48a3-a589-47a19d2f2535/GCF_021165935.1_ASM2116593v1_genomic.fna.gz | prodigal -d GCF_021165935.1_ASM2116593v1_genomic.fna/cds.fna -a GCF_021165935.1_ASM2116593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:42,693] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:42,694] [INFO] Task started: HMMsearch
[2024-01-24 12:47:42,694] [INFO] Running command: hmmsearch --tblout GCF_021165935.1_ASM2116593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference/reference_markers.hmm GCF_021165935.1_ASM2116593v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:42,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:42,988] [INFO] Found 6/6 markers.
[2024-01-24 12:47:43,027] [INFO] Query marker FASTA was written to GCF_021165935.1_ASM2116593v1_genomic.fna/markers.fasta
[2024-01-24 12:47:43,027] [INFO] Task started: Blastn
[2024-01-24 12:47:43,027] [INFO] Running command: blastn -query GCF_021165935.1_ASM2116593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference/reference_markers.fasta -out GCF_021165935.1_ASM2116593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:43,931] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:43,935] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:43,936] [INFO] Target genome list was writen to GCF_021165935.1_ASM2116593v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:43,942] [INFO] Task started: fastANI
[2024-01-24 12:47:43,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7dc837a-fa14-48a3-a589-47a19d2f2535/GCF_021165935.1_ASM2116593v1_genomic.fna.gz --refList GCF_021165935.1_ASM2116593v1_genomic.fna/target_genomes.txt --output GCF_021165935.1_ASM2116593v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:54,589] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:54,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:54,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:54,600] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:54,601] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:54,601] [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_021165935.1	86173	86173	type	True	100.0	1398	1398	95	conclusive
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	99.9534	1355	1398	95	conclusive
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	81.6685	762	1398	95	below_threshold
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	81.5957	753	1398	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	81.391	759	1398	95	below_threshold
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	81.1179	713	1398	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	81.0399	702	1398	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	79.3084	542	1398	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	79.0434	399	1398	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.5033	93	1398	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.7828	84	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:54,602] [INFO] DFAST Taxonomy check result was written to GCF_021165935.1_ASM2116593v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:54,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:54,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:54,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference/checkm_data
[2024-01-24 12:47:54,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:54,653] [INFO] Task started: CheckM
[2024-01-24 12:47:54,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021165935.1_ASM2116593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021165935.1_ASM2116593v1_genomic.fna/checkm_input GCF_021165935.1_ASM2116593v1_genomic.fna/checkm_result
[2024-01-24 12:48:37,426] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:37,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:37,450] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:37,451] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:37,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021165935.1_ASM2116593v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:37,451] [INFO] Task started: Blastn
[2024-01-24 12:48:37,452] [INFO] Running command: blastn -query GCF_021165935.1_ASM2116593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg317087e2-7d05-451c-b599-96a0164b3669/dqc_reference/reference_markers_gtdb.fasta -out GCF_021165935.1_ASM2116593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:38,837] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:38,843] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:38,843] [INFO] Target genome list was writen to GCF_021165935.1_ASM2116593v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:38,853] [INFO] Task started: fastANI
[2024-01-24 12:48:38,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7dc837a-fa14-48a3-a589-47a19d2f2535/GCF_021165935.1_ASM2116593v1_genomic.fna.gz --refList GCF_021165935.1_ASM2116593v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021165935.1_ASM2116593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:49,898] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:49,908] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:48:49,908] [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	87.4379	1161	1398	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	82.045	756	1398	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	82.0256	794	1398	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	82.0012	787	1398	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	81.9735	785	1398	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	81.6486	764	1398	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	81.5549	760	1398	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	81.4924	726	1398	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	81.3998	759	1398	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	81.1398	710	1398	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	79.308	544	1398	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	79.0434	399	1398	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 12:48:49,911] [INFO] GTDB search result was written to GCF_021165935.1_ASM2116593v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:49,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:49,918] [INFO] DFAST_QC result json was written to GCF_021165935.1_ASM2116593v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:49,918] [INFO] DFAST_QC completed!
[2024-01-24 12:48:49,919] [INFO] Total running time: 0h1m22s