[2024-01-25 19:01:05,514] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:05,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:05,516] [INFO] DQC Reference Directory: /var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference
[2024-01-25 19:01:06,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:06,655] [INFO] Task started: Prodigal
[2024-01-25 19:01:06,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e9efbc0-a944-43b2-a8ca-b452fff72945/GCF_030160015.1_ASM3016001v1_genomic.fna.gz | prodigal -d GCF_030160015.1_ASM3016001v1_genomic.fna/cds.fna -a GCF_030160015.1_ASM3016001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:14,007] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:14,008] [INFO] Task started: HMMsearch
[2024-01-25 19:01:14,008] [INFO] Running command: hmmsearch --tblout GCF_030160015.1_ASM3016001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference/reference_markers.hmm GCF_030160015.1_ASM3016001v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:14,200] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:14,201] [INFO] Found 6/6 markers.
[2024-01-25 19:01:14,224] [INFO] Query marker FASTA was written to GCF_030160015.1_ASM3016001v1_genomic.fna/markers.fasta
[2024-01-25 19:01:14,224] [INFO] Task started: Blastn
[2024-01-25 19:01:14,224] [INFO] Running command: blastn -query GCF_030160015.1_ASM3016001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference/reference_markers.fasta -out GCF_030160015.1_ASM3016001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:14,860] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:14,863] [INFO] Selected 32 target genomes.
[2024-01-25 19:01:14,864] [INFO] Target genome list was writen to GCF_030160015.1_ASM3016001v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:14,883] [INFO] Task started: fastANI
[2024-01-25 19:01:14,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e9efbc0-a944-43b2-a8ca-b452fff72945/GCF_030160015.1_ASM3016001v1_genomic.fna.gz --refList GCF_030160015.1_ASM3016001v1_genomic.fna/target_genomes.txt --output GCF_030160015.1_ASM3016001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:33,159] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:33,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:33,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:33,167] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:33,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:33,167] [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
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	77.3845	145	901	95	below_threshold
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	76.9942	151	901	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7028	57	901	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.4122	86	901	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	76.4058	53	901	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.1644	60	901	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.0173	63	901	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	75.8108	52	901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:33,169] [INFO] DFAST Taxonomy check result was written to GCF_030160015.1_ASM3016001v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:33,169] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:33,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:33,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference/checkm_data
[2024-01-25 19:01:33,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:33,200] [INFO] Task started: CheckM
[2024-01-25 19:01:33,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160015.1_ASM3016001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160015.1_ASM3016001v1_genomic.fna/checkm_input GCF_030160015.1_ASM3016001v1_genomic.fna/checkm_result
[2024-01-25 19:01:58,457] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:58,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:58,478] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:58,478] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:58,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160015.1_ASM3016001v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:58,479] [INFO] Task started: Blastn
[2024-01-25 19:01:58,479] [INFO] Running command: blastn -query GCF_030160015.1_ASM3016001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge592b6e9-7ba8-4382-b0f0-655bf785997b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160015.1_ASM3016001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:59,593] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:59,596] [INFO] Selected 31 target genomes.
[2024-01-25 19:01:59,596] [INFO] Target genome list was writen to GCF_030160015.1_ASM3016001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:59,628] [INFO] Task started: fastANI
[2024-01-25 19:01:59,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e9efbc0-a944-43b2-a8ca-b452fff72945/GCF_030160015.1_ASM3016001v1_genomic.fna.gz --refList GCF_030160015.1_ASM3016001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160015.1_ASM3016001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:16,780] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:16,788] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:02:16,789] [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_009184395.1	s__Amylibacter sp009184395	77.549	79	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742285.1	s__Amylibacter kogurei	77.3854	145	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469545.1	s__Amylibacter sp002469545	77.0182	66	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652655.1	s__Amylibacter ulvae	76.9952	150	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764475.1	s__Amylibacter sp016764475	76.8728	82	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	76.6505	58	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184935.1	s__Actibacterium_A lipolyticum	76.4447	52	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	76.4312	84	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.3698	52	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719615.1	s__Amylibacter sediminis	76.3281	100	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223125.1	s__Amylibacter sp018223125	76.2333	88	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	75.7161	54	901	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:16,790] [INFO] GTDB search result was written to GCF_030160015.1_ASM3016001v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:16,790] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:16,793] [INFO] DFAST_QC result json was written to GCF_030160015.1_ASM3016001v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:16,793] [INFO] DFAST_QC completed!
[2024-01-25 19:02:16,794] [INFO] Total running time: 0h1m11s