[2024-01-24 12:29:52,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference
[2024-01-24 12:29:53,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,843] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e3c5401-a09c-4ebd-a695-7901fb938d20/GCF_017254865.1_ASM1725486v1_genomic.fna.gz | prodigal -d GCF_017254865.1_ASM1725486v1_genomic.fna/cds.fna -a GCF_017254865.1_ASM1725486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:07,732] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:07,732] [INFO] Task started: HMMsearch
[2024-01-24 12:30:07,732] [INFO] Running command: hmmsearch --tblout GCF_017254865.1_ASM1725486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference/reference_markers.hmm GCF_017254865.1_ASM1725486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:08,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:08,018] [INFO] Found 6/6 markers.
[2024-01-24 12:30:08,059] [INFO] Query marker FASTA was written to GCF_017254865.1_ASM1725486v1_genomic.fna/markers.fasta
[2024-01-24 12:30:08,059] [INFO] Task started: Blastn
[2024-01-24 12:30:08,060] [INFO] Running command: blastn -query GCF_017254865.1_ASM1725486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference/reference_markers.fasta -out GCF_017254865.1_ASM1725486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:08,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:08,819] [INFO] Selected 21 target genomes.
[2024-01-24 12:30:08,819] [INFO] Target genome list was writen to GCF_017254865.1_ASM1725486v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:08,829] [INFO] Task started: fastANI
[2024-01-24 12:30:08,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3c5401-a09c-4ebd-a695-7901fb938d20/GCF_017254865.1_ASM1725486v1_genomic.fna.gz --refList GCF_017254865.1_ASM1725486v1_genomic.fna/target_genomes.txt --output GCF_017254865.1_ASM1725486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:24,079] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:24,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:24,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:24,089] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:24,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:24,090] [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
Bowmanella dokdonensis	strain=JCM 30855	GCA_017254865.1	751969	751969	type	True	100.0	1549	1550	95	conclusive
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	77.9932	310	1550	95	below_threshold
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	77.3287	256	1550	95	below_threshold
Lacimicrobium alkaliphilum	strain=CGMCC 1.12923	GCA_014640135.1	1526571	1526571	type	True	77.2555	263	1550	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	77.1746	106	1550	95	below_threshold
Saliniradius amylolyticus	strain=HMF8227	GCA_003143555.1	2183582	2183582	type	True	77.0062	193	1550	95	below_threshold
Aeromonas diversa	strain=CECT 4254	GCA_000819805.1	502790	502790	type	True	76.4057	73	1550	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.2762	74	1550	95	below_threshold
Aeromonas diversa	strain=2478-85	GCA_000367845.1	502790	502790	type	True	76.1608	75	1550	95	below_threshold
Sodalis ligni	strain=dw23	GCA_016865525.2	2697027	2697027	type	True	75.7178	52	1550	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.6677	63	1550	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	75.542	53	1550	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:24,091] [INFO] DFAST Taxonomy check result was written to GCF_017254865.1_ASM1725486v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:24,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:24,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:24,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference/checkm_data
[2024-01-24 12:30:24,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:24,142] [INFO] Task started: CheckM
[2024-01-24 12:30:24,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017254865.1_ASM1725486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017254865.1_ASM1725486v1_genomic.fna/checkm_input GCF_017254865.1_ASM1725486v1_genomic.fna/checkm_result
[2024-01-24 12:31:07,509] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:07,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:07,537] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:07,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:07,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017254865.1_ASM1725486v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:07,538] [INFO] Task started: Blastn
[2024-01-24 12:31:07,538] [INFO] Running command: blastn -query GCF_017254865.1_ASM1725486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb69ed004-f4e1-446e-904f-14f1a4b99b1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017254865.1_ASM1725486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:08,789] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:08,794] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:08,794] [INFO] Target genome list was writen to GCF_017254865.1_ASM1725486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:08,808] [INFO] Task started: fastANI
[2024-01-24 12:31:08,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3c5401-a09c-4ebd-a695-7901fb938d20/GCF_017254865.1_ASM1725486v1_genomic.fna.gz --refList GCF_017254865.1_ASM1725486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017254865.1_ASM1725486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:24,830] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:24,848] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:24,848] [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_017254865.1	s__Bowmanella dokdonensis	100.0	1549	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002887595.1	s__Bowmanella denitrificans	78.0508	393	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645355.1	s__Bowmanella pacifica	78.0049	309	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531185.1	s__Bowmanella sp018531185	77.98	319	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_002201535.1	s__Lacimicrobium sp002201535	77.6887	234	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	77.6552	348	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591895.1	s__Lacimicrobium alkaliphilum	77.339	255	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003075035.1	s__Zobellella_A maritima	77.1052	93	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143555.1	s__Saliniradius amylolyticus	77.0062	193	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Saliniradius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644725.1	s__Alteromonas sp015644725	76.6467	87	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819805.1	s__Aeromonas diversa	76.3857	74	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.98	99.98	0.99	0.99	2	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	76.3112	125	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012775.1	s__Zobellella_C endophytica	76.2316	108	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237365.1	s__Zobellella denitrificans	76.2199	101	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_010131535.1	s__Acerihabitans arboris	75.7589	55	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865525.2	s__Acerihabitans sp004346745	75.7322	51	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	98.11	98.11	0.88	0.88	2	-
GCF_900129905.1	s__Ferrimonas marina	75.7179	78	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:24,850] [INFO] GTDB search result was written to GCF_017254865.1_ASM1725486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:24,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:24,853] [INFO] DFAST_QC result json was written to GCF_017254865.1_ASM1725486v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:24,853] [INFO] DFAST_QC completed!
[2024-01-24 12:31:24,853] [INFO] Total running time: 0h1m32s