[2023-06-30 11:27:23,330] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:27:23,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:27:23,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference
[2023-06-30 11:27:24,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:27:24,488] [INFO] Task started: Prodigal
[2023-06-30 11:27:24,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc837514-7c7a-456d-b026-81f5b4c9ef4a/GCA_025541255.1_ASM2554125v1_genomic.fna.gz | prodigal -d GCA_025541255.1_ASM2554125v1_genomic.fna/cds.fna -a GCA_025541255.1_ASM2554125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:27:41,951] [INFO] Task succeeded: Prodigal
[2023-06-30 11:27:41,951] [INFO] Task started: HMMsearch
[2023-06-30 11:27:41,951] [INFO] Running command: hmmsearch --tblout GCA_025541255.1_ASM2554125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference/reference_markers.hmm GCA_025541255.1_ASM2554125v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:27:42,154] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:27:42,155] [INFO] Found 6/6 markers.
[2023-06-30 11:27:42,185] [INFO] Query marker FASTA was written to GCA_025541255.1_ASM2554125v1_genomic.fna/markers.fasta
[2023-06-30 11:27:42,186] [INFO] Task started: Blastn
[2023-06-30 11:27:42,186] [INFO] Running command: blastn -query GCA_025541255.1_ASM2554125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference/reference_markers.fasta -out GCA_025541255.1_ASM2554125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:27:42,749] [INFO] Task succeeded: Blastn
[2023-06-30 11:27:42,753] [INFO] Selected 8 target genomes.
[2023-06-30 11:27:42,753] [INFO] Target genome list was writen to GCA_025541255.1_ASM2554125v1_genomic.fna/target_genomes.txt
[2023-06-30 11:27:42,754] [INFO] Task started: fastANI
[2023-06-30 11:27:42,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc837514-7c7a-456d-b026-81f5b4c9ef4a/GCA_025541255.1_ASM2554125v1_genomic.fna.gz --refList GCA_025541255.1_ASM2554125v1_genomic.fna/target_genomes.txt --output GCA_025541255.1_ASM2554125v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:27:49,569] [INFO] Task succeeded: fastANI
[2023-06-30 11:27:49,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:27:49,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:27:49,577] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2023-06-30 11:27:49,577] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-30 11:27:49,577] [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 faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	97.7412	667	773	95	inconclusive
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	97.7254	671	773	95	inconclusive
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	97.7179	672	773	95	inconclusive
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	95.2162	670	773	95	inconclusive
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	95.1466	675	773	95	inconclusive
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	91.0081	600	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:27:49,579] [INFO] DFAST Taxonomy check result was written to GCA_025541255.1_ASM2554125v1_genomic.fna/tc_result.tsv
[2023-06-30 11:27:49,579] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:27:49,579] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:27:49,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference/checkm_data
[2023-06-30 11:27:49,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:27:49,616] [INFO] Task started: CheckM
[2023-06-30 11:27:49,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025541255.1_ASM2554125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025541255.1_ASM2554125v1_genomic.fna/checkm_input GCA_025541255.1_ASM2554125v1_genomic.fna/checkm_result
[2023-06-30 11:28:40,383] [INFO] Task succeeded: CheckM
[2023-06-30 11:28:40,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:28:40,402] [INFO] ===== Completeness check finished =====
[2023-06-30 11:28:40,402] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:28:40,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025541255.1_ASM2554125v1_genomic.fna/markers.fasta)
[2023-06-30 11:28:40,402] [INFO] Task started: Blastn
[2023-06-30 11:28:40,403] [INFO] Running command: blastn -query GCA_025541255.1_ASM2554125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf3ee045-b153-4616-a5b5-fcf32e139d3e/dqc_reference/reference_markers_gtdb.fasta -out GCA_025541255.1_ASM2554125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:28:41,150] [INFO] Task succeeded: Blastn
[2023-06-30 11:28:41,154] [INFO] Selected 9 target genomes.
[2023-06-30 11:28:41,154] [INFO] Target genome list was writen to GCA_025541255.1_ASM2554125v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:28:41,155] [INFO] Task started: fastANI
[2023-06-30 11:28:41,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc837514-7c7a-456d-b026-81f5b4c9ef4a/GCA_025541255.1_ASM2554125v1_genomic.fna.gz --refList GCA_025541255.1_ASM2554125v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025541255.1_ASM2554125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:28:48,075] [INFO] Task succeeded: fastANI
[2023-06-30 11:28:48,083] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-30 11:28:48,083] [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_014647335.1	s__Butyricimonas faecihominis	97.7179	672	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	inconclusive
GCF_011927845.1	s__Butyricimonas paravirosa	95.1466	675	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	inconclusive
GCF_000519105.1	s__Butyricimonas virosa	91.0891	597	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCA_019117165.1	s__Butyricimonas faecavium	87.1632	459	773	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	86.883	528	773	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	83.3209	472	773	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	81.3551	481	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-30 11:28:48,085] [INFO] GTDB search result was written to GCA_025541255.1_ASM2554125v1_genomic.fna/result_gtdb.tsv
[2023-06-30 11:28:48,086] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:28:48,089] [INFO] DFAST_QC result json was written to GCA_025541255.1_ASM2554125v1_genomic.fna/dqc_result.json
[2023-06-30 11:28:48,089] [INFO] DFAST_QC completed!
[2023-06-30 11:28:48,089] [INFO] Total running time: 0h1m25s