[2024-01-24 12:23:03,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference
[2024-01-24 12:23:04,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,691] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f245ee4-2dc9-4f12-84ab-792dccbbb49d/GCF_003194565.2_ASM319456v2_genomic.fna.gz | prodigal -d GCF_003194565.2_ASM319456v2_genomic.fna/cds.fna -a GCF_003194565.2_ASM319456v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:10,282] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:10,282] [INFO] Task started: HMMsearch
[2024-01-24 12:23:10,282] [INFO] Running command: hmmsearch --tblout GCF_003194565.2_ASM319456v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference/reference_markers.hmm GCF_003194565.2_ASM319456v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:10,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:10,537] [INFO] Found 6/6 markers.
[2024-01-24 12:23:10,567] [INFO] Query marker FASTA was written to GCF_003194565.2_ASM319456v2_genomic.fna/markers.fasta
[2024-01-24 12:23:10,568] [INFO] Task started: Blastn
[2024-01-24 12:23:10,568] [INFO] Running command: blastn -query GCF_003194565.2_ASM319456v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference/reference_markers.fasta -out GCF_003194565.2_ASM319456v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:11,281] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:11,285] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:11,285] [INFO] Target genome list was writen to GCF_003194565.2_ASM319456v2_genomic.fna/target_genomes.txt
[2024-01-24 12:23:11,294] [INFO] Task started: fastANI
[2024-01-24 12:23:11,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f245ee4-2dc9-4f12-84ab-792dccbbb49d/GCF_003194565.2_ASM319456v2_genomic.fna.gz --refList GCF_003194565.2_ASM319456v2_genomic.fna/target_genomes.txt --output GCF_003194565.2_ASM319456v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:22,220] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:22,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:22,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:22,228] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:22,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:22,228] [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
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	100.0	838	840	95	conclusive
Kangiella geojedonensis	strain=YCS-5	GCA_000981765.1	914150	914150	type	True	80.2088	404	840	95	below_threshold
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	80.1547	393	840	95	below_threshold
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	79.7263	232	840	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	79.2309	284	840	95	below_threshold
Kangiella aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	78.7838	158	840	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	78.4899	171	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:22,230] [INFO] DFAST Taxonomy check result was written to GCF_003194565.2_ASM319456v2_genomic.fna/tc_result.tsv
[2024-01-24 12:23:22,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:22,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:22,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference/checkm_data
[2024-01-24 12:23:22,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:22,265] [INFO] Task started: CheckM
[2024-01-24 12:23:22,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003194565.2_ASM319456v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003194565.2_ASM319456v2_genomic.fna/checkm_input GCF_003194565.2_ASM319456v2_genomic.fna/checkm_result
[2024-01-24 12:23:45,522] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:45,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:45,547] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:45,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:45,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003194565.2_ASM319456v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:45,549] [INFO] Task started: Blastn
[2024-01-24 12:23:45,549] [INFO] Running command: blastn -query GCF_003194565.2_ASM319456v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aac35b0-878b-4d43-be1a-e48ea45e5cdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_003194565.2_ASM319456v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:46,667] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:46,672] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:46,672] [INFO] Target genome list was writen to GCF_003194565.2_ASM319456v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:46,692] [INFO] Task started: fastANI
[2024-01-24 12:23:46,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f245ee4-2dc9-4f12-84ab-792dccbbb49d/GCF_003194565.2_ASM319456v2_genomic.fna.gz --refList GCF_003194565.2_ASM319456v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003194565.2_ASM319456v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:57,037] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:57,053] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:57,053] [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_003194565.2	s__Kangiella spongicola	100.0	838	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	conclusive
GCF_000981765.1	s__Kangiella geojedonensis	80.2088	404	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003370465.1	s__Kangiella sp003370465	79.9955	215	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708405.1	s__Kangiella sediminilitoris	79.731	231	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374105.1	s__Kangiella aquimarina	78.8007	159	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024085.1	s__Kangiella koreensis	78.5128	170	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002838765.1	s__Kangiella profundi	78.4728	158	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014762745.1	s__Kangiella sp014762745	78.4655	154	840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:57,055] [INFO] GTDB search result was written to GCF_003194565.2_ASM319456v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:57,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:57,060] [INFO] DFAST_QC result json was written to GCF_003194565.2_ASM319456v2_genomic.fna/dqc_result.json
[2024-01-24 12:23:57,060] [INFO] DFAST_QC completed!
[2024-01-24 12:23:57,061] [INFO] Total running time: 0h0m54s