[2024-01-24 15:18:19,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,591] [INFO] DQC Reference Directory: /var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference
[2024-01-24 15:18:20,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,836] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg46df2211-9034-4085-a58d-c6f1a65642c7/GCF_003991565.1_ASM399156v1_genomic.fna.gz | prodigal -d GCF_003991565.1_ASM399156v1_genomic.fna/cds.fna -a GCF_003991565.1_ASM399156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:47,361] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:47,361] [INFO] Task started: HMMsearch
[2024-01-24 15:18:47,361] [INFO] Running command: hmmsearch --tblout GCF_003991565.1_ASM399156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference/reference_markers.hmm GCF_003991565.1_ASM399156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:47,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:47,664] [INFO] Found 6/6 markers.
[2024-01-24 15:18:47,718] [INFO] Query marker FASTA was written to GCF_003991565.1_ASM399156v1_genomic.fna/markers.fasta
[2024-01-24 15:18:47,718] [INFO] Task started: Blastn
[2024-01-24 15:18:47,719] [INFO] Running command: blastn -query GCF_003991565.1_ASM399156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference/reference_markers.fasta -out GCF_003991565.1_ASM399156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:48,384] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:48,388] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:48,389] [INFO] Target genome list was writen to GCF_003991565.1_ASM399156v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:48,395] [INFO] Task started: fastANI
[2024-01-24 15:18:48,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg46df2211-9034-4085-a58d-c6f1a65642c7/GCF_003991565.1_ASM399156v1_genomic.fna.gz --refList GCF_003991565.1_ASM399156v1_genomic.fna/target_genomes.txt --output GCF_003991565.1_ASM399156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:00,548] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:00,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:00,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:00,557] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:00,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:00,557] [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 faecalis	strain=H184	GCA_003991565.1	2093856	2093856	type	True	100.0	1653	1658	95	conclusive
Butyricimonas faecalis	strain=vagina	GCA_900258545.1	2093856	2093856	type	True	99.566	1476	1658	95	conclusive
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	87.8441	922	1658	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	87.76	907	1658	95	below_threshold
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	87.7395	905	1658	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	87.6949	1001	1658	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	87.6895	913	1658	95	below_threshold
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	87.6613	1004	1658	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	87.6587	909	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:00,559] [INFO] DFAST Taxonomy check result was written to GCF_003991565.1_ASM399156v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:00,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:00,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:00,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference/checkm_data
[2024-01-24 15:19:00,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:00,631] [INFO] Task started: CheckM
[2024-01-24 15:19:00,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003991565.1_ASM399156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003991565.1_ASM399156v1_genomic.fna/checkm_input GCF_003991565.1_ASM399156v1_genomic.fna/checkm_result
[2024-01-24 15:20:14,103] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:14,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:14,126] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:14,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:14,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003991565.1_ASM399156v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:14,128] [INFO] Task started: Blastn
[2024-01-24 15:20:14,128] [INFO] Running command: blastn -query GCF_003991565.1_ASM399156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc23d4d20-7434-429a-b31d-937e405ae869/dqc_reference/reference_markers_gtdb.fasta -out GCF_003991565.1_ASM399156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:14,900] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:14,904] [INFO] Selected 7 target genomes.
[2024-01-24 15:20:14,904] [INFO] Target genome list was writen to GCF_003991565.1_ASM399156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:14,919] [INFO] Task started: fastANI
[2024-01-24 15:20:14,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg46df2211-9034-4085-a58d-c6f1a65642c7/GCF_003991565.1_ASM399156v1_genomic.fna.gz --refList GCF_003991565.1_ASM399156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003991565.1_ASM399156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:23,115] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:23,129] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:23,130] [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_003991565.1	s__Butyricimonas faecalis	100.0	1655	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	conclusive
GCF_000519105.1	s__Butyricimonas virosa	87.7934	905	1658	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	87.6477	1005	1658	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	87.6442	910	1658	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	86.6064	669	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761485.1	s__Butyricimonas sp900761485	82.4358	685	1658	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	81.7187	755	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:23,132] [INFO] GTDB search result was written to GCF_003991565.1_ASM399156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:23,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:23,138] [INFO] DFAST_QC result json was written to GCF_003991565.1_ASM399156v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:23,138] [INFO] DFAST_QC completed!
[2024-01-24 15:20:23,138] [INFO] Total running time: 0h2m4s