[2024-01-24 12:31:20,776] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:20,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:20,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference
[2024-01-24 12:31:22,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,042] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,042] [INFO] Running command: gunzip -c /var/lib/cwl/stged7629de-471a-44f6-b813-f897062bb51d/GCF_024741215.1_ASM2474121v1_genomic.fna.gz | prodigal -d GCF_024741215.1_ASM2474121v1_genomic.fna/cds.fna -a GCF_024741215.1_ASM2474121v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:37,529] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:37,529] [INFO] Task started: HMMsearch
[2024-01-24 12:31:37,529] [INFO] Running command: hmmsearch --tblout GCF_024741215.1_ASM2474121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference/reference_markers.hmm GCF_024741215.1_ASM2474121v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:37,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:37,746] [INFO] Found 6/6 markers.
[2024-01-24 12:31:37,773] [INFO] Query marker FASTA was written to GCF_024741215.1_ASM2474121v1_genomic.fna/markers.fasta
[2024-01-24 12:31:37,773] [INFO] Task started: Blastn
[2024-01-24 12:31:37,773] [INFO] Running command: blastn -query GCF_024741215.1_ASM2474121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference/reference_markers.fasta -out GCF_024741215.1_ASM2474121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:38,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:38,339] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:38,340] [INFO] Target genome list was writen to GCF_024741215.1_ASM2474121v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:38,345] [INFO] Task started: fastANI
[2024-01-24 12:31:38,345] [INFO] Running command: fastANI --query /var/lib/cwl/stged7629de-471a-44f6-b813-f897062bb51d/GCF_024741215.1_ASM2474121v1_genomic.fna.gz --refList GCF_024741215.1_ASM2474121v1_genomic.fna/target_genomes.txt --output GCF_024741215.1_ASM2474121v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:47,996] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:47,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:47,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:48,006] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:48,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:48,007] [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
Sanguibacteroides justesenii	strain=OUH 308042	GCA_000832075.1	1547597	1547597	type	True	96.1213	965	1116	95	conclusive
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	78.1736	206	1116	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	78.1055	205	1116	95	below_threshold
Butyricimonas faecalis	strain=vagina	GCA_900258545.1	2093856	2093856	type	True	78.0084	198	1116	95	below_threshold
Butyricimonas faecalis	strain=H184	GCA_003991565.1	2093856	2093856	type	True	77.9919	198	1116	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	77.8984	193	1116	95	below_threshold
Butyricimonas synergistica	strain=DSM 23225	GCA_000379665.1	544644	544644	type	True	77.7457	204	1116	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	77.6722	195	1116	95	below_threshold
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	77.6414	220	1116	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	77.6354	215	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,008] [INFO] DFAST Taxonomy check result was written to GCF_024741215.1_ASM2474121v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:48,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:48,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:48,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference/checkm_data
[2024-01-24 12:31:48,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:48,044] [INFO] Task started: CheckM
[2024-01-24 12:31:48,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024741215.1_ASM2474121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024741215.1_ASM2474121v1_genomic.fna/checkm_input GCF_024741215.1_ASM2474121v1_genomic.fna/checkm_result
[2024-01-24 12:32:32,227] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:32,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:32,245] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:32,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:32,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024741215.1_ASM2474121v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:32,246] [INFO] Task started: Blastn
[2024-01-24 12:32:32,246] [INFO] Running command: blastn -query GCF_024741215.1_ASM2474121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3949cd7e-7fad-4ad5-8209-4d3667cb1276/dqc_reference/reference_markers_gtdb.fasta -out GCF_024741215.1_ASM2474121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:33,024] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:33,029] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:33,030] [INFO] Target genome list was writen to GCF_024741215.1_ASM2474121v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:33,042] [INFO] Task started: fastANI
[2024-01-24 12:32:33,042] [INFO] Running command: fastANI --query /var/lib/cwl/stged7629de-471a-44f6-b813-f897062bb51d/GCF_024741215.1_ASM2474121v1_genomic.fna.gz --refList GCF_024741215.1_ASM2474121v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024741215.1_ASM2474121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:43,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:43,607] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:43,607] [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
GCA_001487125.1	s__Gabonibacter massiliensis	96.3002	982	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Gabonibacter	95.0	98.83	98.37	0.92	0.88	5	conclusive
GCA_900543425.1	s__Gabonibacter sp900543425	87.4681	894	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Gabonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647335.1	s__Butyricimonas faecihominis	78.1563	206	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCF_003991565.1	s__Butyricimonas faecalis	78.0094	197	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	-
GCA_900761485.1	s__Butyricimonas sp900761485	77.9013	176	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479425.1	s__Butyricimonas sp003479425	77.8092	208	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
GCF_000379665.1	s__Butyricimonas synergistica	77.7301	205	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.02	98.02	0.85	0.85	3	-
GCF_000519105.1	s__Butyricimonas virosa	77.6723	195	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCF_011927845.1	s__Butyricimonas paravirosa	77.62	221	1116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:43,609] [INFO] GTDB search result was written to GCF_024741215.1_ASM2474121v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:43,609] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:43,612] [INFO] DFAST_QC result json was written to GCF_024741215.1_ASM2474121v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:43,612] [INFO] DFAST_QC completed!
[2024-01-24 12:32:43,612] [INFO] Total running time: 0h1m23s