[2024-01-25 20:00:20,470] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:20,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:20,474] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference
[2024-01-25 20:00:21,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:21,619] [INFO] Task started: Prodigal
[2024-01-25 20:00:21,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg13d98eb5-927a-46f8-8b25-439410001ae0/GCF_025148635.1_ASM2514863v1_genomic.fna.gz | prodigal -d GCF_025148635.1_ASM2514863v1_genomic.fna/cds.fna -a GCF_025148635.1_ASM2514863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:42,314] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:42,314] [INFO] Task started: HMMsearch
[2024-01-25 20:00:42,314] [INFO] Running command: hmmsearch --tblout GCF_025148635.1_ASM2514863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference/reference_markers.hmm GCF_025148635.1_ASM2514863v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:42,597] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:42,598] [INFO] Found 6/6 markers.
[2024-01-25 20:00:42,636] [INFO] Query marker FASTA was written to GCF_025148635.1_ASM2514863v1_genomic.fna/markers.fasta
[2024-01-25 20:00:42,637] [INFO] Task started: Blastn
[2024-01-25 20:00:42,637] [INFO] Running command: blastn -query GCF_025148635.1_ASM2514863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference/reference_markers.fasta -out GCF_025148635.1_ASM2514863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:43,199] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:43,201] [INFO] Selected 11 target genomes.
[2024-01-25 20:00:43,202] [INFO] Target genome list was writen to GCF_025148635.1_ASM2514863v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:43,213] [INFO] Task started: fastANI
[2024-01-25 20:00:43,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d98eb5-927a-46f8-8b25-439410001ae0/GCF_025148635.1_ASM2514863v1_genomic.fna.gz --refList GCF_025148635.1_ASM2514863v1_genomic.fna/target_genomes.txt --output GCF_025148635.1_ASM2514863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:54,635] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:54,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:54,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:54,642] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:00:54,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:54,643] [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
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	100.0	1603	1604	95	conclusive
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	99.9412	1533	1604	95	conclusive
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	91.7903	1121	1604	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	91.7816	1116	1604	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	91.1654	1084	1604	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	91.129	1080	1604	95	below_threshold
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	91.0877	1086	1604	95	below_threshold
Butyricimonas faecalis	strain=vagina	GCA_900258545.1	2093856	2093856	type	True	87.8337	919	1604	95	below_threshold
Butyricimonas faecalis	strain=H184	GCA_003991565.1	2093856	2093856	type	True	87.8182	941	1604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:54,644] [INFO] DFAST Taxonomy check result was written to GCF_025148635.1_ASM2514863v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:54,645] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:54,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:54,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference/checkm_data
[2024-01-25 20:00:54,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:54,692] [INFO] Task started: CheckM
[2024-01-25 20:00:54,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025148635.1_ASM2514863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025148635.1_ASM2514863v1_genomic.fna/checkm_input GCF_025148635.1_ASM2514863v1_genomic.fna/checkm_result
[2024-01-25 20:01:52,503] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:52,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:52,520] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:52,520] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:52,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025148635.1_ASM2514863v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:52,521] [INFO] Task started: Blastn
[2024-01-25 20:01:52,521] [INFO] Running command: blastn -query GCF_025148635.1_ASM2514863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa053d6-c260-4123-a12b-b3b9ca53edf4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025148635.1_ASM2514863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:53,351] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:53,353] [INFO] Selected 7 target genomes.
[2024-01-25 20:01:53,353] [INFO] Target genome list was writen to GCF_025148635.1_ASM2514863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:53,359] [INFO] Task started: fastANI
[2024-01-25 20:01:53,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d98eb5-927a-46f8-8b25-439410001ae0/GCF_025148635.1_ASM2514863v1_genomic.fna.gz --refList GCF_025148635.1_ASM2514863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025148635.1_ASM2514863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:01,677] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:01,683] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:01,683] [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_000519105.1	s__Butyricimonas virosa	99.9412	1533	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	conclusive
GCF_011927845.1	s__Butyricimonas paravirosa	91.8214	1119	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	-
GCF_014647335.1	s__Butyricimonas faecihominis	91.1314	1079	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCA_019117165.1	s__Butyricimonas faecavium	89.1737	761	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991565.1	s__Butyricimonas faecalis	87.8175	941	1604	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	83.1269	767	1604	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	82.6086	899	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:01,684] [INFO] GTDB search result was written to GCF_025148635.1_ASM2514863v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:01,685] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:01,687] [INFO] DFAST_QC result json was written to GCF_025148635.1_ASM2514863v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:01,687] [INFO] DFAST_QC completed!
[2024-01-25 20:02:01,687] [INFO] Total running time: 0h1m41s