[2024-01-24 13:48:59,269] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference
[2024-01-24 13:49:00,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,577] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg29c55909-8009-48be-9ae6-ffe966c3a563/GCF_000024085.1_ASM2408v1_genomic.fna.gz | prodigal -d GCF_000024085.1_ASM2408v1_genomic.fna/cds.fna -a GCF_000024085.1_ASM2408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:07,855] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:07,856] [INFO] Task started: HMMsearch
[2024-01-24 13:49:07,856] [INFO] Running command: hmmsearch --tblout GCF_000024085.1_ASM2408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference/reference_markers.hmm GCF_000024085.1_ASM2408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:08,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:08,129] [INFO] Found 6/6 markers.
[2024-01-24 13:49:08,158] [INFO] Query marker FASTA was written to GCF_000024085.1_ASM2408v1_genomic.fna/markers.fasta
[2024-01-24 13:49:08,159] [INFO] Task started: Blastn
[2024-01-24 13:49:08,159] [INFO] Running command: blastn -query GCF_000024085.1_ASM2408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference/reference_markers.fasta -out GCF_000024085.1_ASM2408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:08,914] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:08,917] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:08,917] [INFO] Target genome list was writen to GCF_000024085.1_ASM2408v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:08,928] [INFO] Task started: fastANI
[2024-01-24 13:49:08,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c55909-8009-48be-9ae6-ffe966c3a563/GCF_000024085.1_ASM2408v1_genomic.fna.gz --refList GCF_000024085.1_ASM2408v1_genomic.fna/target_genomes.txt --output GCF_000024085.1_ASM2408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:19,779] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:19,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:19,788] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:19,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:19,789] [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 koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	100.0	950	950	95	conclusive
Kangiella aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	82.1476	630	950	95	below_threshold
Kangiella profundi	strain=FT102	GCA_002838765.1	1561924	1561924	type	True	81.9884	601	950	95	below_threshold
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	81.8869	616	950	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	78.6876	161	950	95	below_threshold
Kangiella geojedonensis	strain=YCS-5	GCA_000981765.1	914150	914150	type	True	78.4213	151	950	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	77.4907	183	950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,790] [INFO] DFAST Taxonomy check result was written to GCF_000024085.1_ASM2408v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:19,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:19,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:19,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference/checkm_data
[2024-01-24 13:49:19,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:19,826] [INFO] Task started: CheckM
[2024-01-24 13:49:19,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024085.1_ASM2408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024085.1_ASM2408v1_genomic.fna/checkm_input GCF_000024085.1_ASM2408v1_genomic.fna/checkm_result
[2024-01-24 13:49:48,316] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:48,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:48,340] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:48,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:48,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024085.1_ASM2408v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:48,341] [INFO] Task started: Blastn
[2024-01-24 13:49:48,341] [INFO] Running command: blastn -query GCF_000024085.1_ASM2408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbad8b2f7-aa89-4ddf-a383-ef023419c782/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024085.1_ASM2408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:49,526] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:49,529] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:49,529] [INFO] Target genome list was writen to GCF_000024085.1_ASM2408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:49,566] [INFO] Task started: fastANI
[2024-01-24 13:49:49,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c55909-8009-48be-9ae6-ffe966c3a563/GCF_000024085.1_ASM2408v1_genomic.fna.gz --refList GCF_000024085.1_ASM2408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024085.1_ASM2408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:57,437] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,445] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:57,445] [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_000024085.1	s__Kangiella koreensis	100.0	950	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014762745.1	s__Kangiella sp014762745	82.5283	616	950	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	82.1532	629	950	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	81.9688	601	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194565.2	s__Kangiella spongicola	78.6883	161	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	-
GCF_000981765.1	s__Kangiella geojedonensis	78.4213	151	950	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	77.8474	91	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674675.1	s__Kangiella sp009674675	77.504	114	950	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 13:49:57,446] [INFO] GTDB search result was written to GCF_000024085.1_ASM2408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:57,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:57,450] [INFO] DFAST_QC result json was written to GCF_000024085.1_ASM2408v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:57,450] [INFO] DFAST_QC completed!
[2024-01-24 13:49:57,450] [INFO] Total running time: 0h0m58s