[2024-01-24 12:42:09,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference
[2024-01-24 12:42:10,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,537] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg924e8581-8d85-49cf-a5e9-06bcf841bacf/GCF_004801455.1_ASM480145v1_genomic.fna.gz | prodigal -d GCF_004801455.1_ASM480145v1_genomic.fna/cds.fna -a GCF_004801455.1_ASM480145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:21,115] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:21,116] [INFO] Task started: HMMsearch
[2024-01-24 12:42:21,116] [INFO] Running command: hmmsearch --tblout GCF_004801455.1_ASM480145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference/reference_markers.hmm GCF_004801455.1_ASM480145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:21,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:21,431] [INFO] Found 6/6 markers.
[2024-01-24 12:42:21,483] [INFO] Query marker FASTA was written to GCF_004801455.1_ASM480145v1_genomic.fna/markers.fasta
[2024-01-24 12:42:21,483] [INFO] Task started: Blastn
[2024-01-24 12:42:21,484] [INFO] Running command: blastn -query GCF_004801455.1_ASM480145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference/reference_markers.fasta -out GCF_004801455.1_ASM480145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:22,084] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:22,089] [INFO] Selected 13 target genomes.
[2024-01-24 12:42:22,089] [INFO] Target genome list was writen to GCF_004801455.1_ASM480145v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:22,094] [INFO] Task started: fastANI
[2024-01-24 12:42:22,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg924e8581-8d85-49cf-a5e9-06bcf841bacf/GCF_004801455.1_ASM480145v1_genomic.fna.gz --refList GCF_004801455.1_ASM480145v1_genomic.fna/target_genomes.txt --output GCF_004801455.1_ASM480145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:36,436] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:36,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:36,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:36,451] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:36,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:36,452] [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
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	100.0	1795	1798	95	conclusive
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	99.9956	1796	1798	95	conclusive
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	80.8712	864	1798	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	79.2113	492	1798	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	78.8943	462	1798	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	78.8739	510	1798	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	78.8698	476	1798	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	78.7396	492	1798	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.6543	166	1798	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.03	149	1798	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.6967	106	1798	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.6152	114	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:36,454] [INFO] DFAST Taxonomy check result was written to GCF_004801455.1_ASM480145v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:36,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:36,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:36,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference/checkm_data
[2024-01-24 12:42:36,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:36,508] [INFO] Task started: CheckM
[2024-01-24 12:42:36,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801455.1_ASM480145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801455.1_ASM480145v1_genomic.fna/checkm_input GCF_004801455.1_ASM480145v1_genomic.fna/checkm_result
[2024-01-24 12:43:12,879] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:12,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:12,905] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:12,905] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:12,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801455.1_ASM480145v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:12,906] [INFO] Task started: Blastn
[2024-01-24 12:43:12,906] [INFO] Running command: blastn -query GCF_004801455.1_ASM480145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg867d630a-63b9-4908-8af0-da21946bec4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801455.1_ASM480145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:13,699] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:13,705] [INFO] Selected 12 target genomes.
[2024-01-24 12:43:13,705] [INFO] Target genome list was writen to GCF_004801455.1_ASM480145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:13,714] [INFO] Task started: fastANI
[2024-01-24 12:43:13,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg924e8581-8d85-49cf-a5e9-06bcf841bacf/GCF_004801455.1_ASM480145v1_genomic.fna.gz --refList GCF_004801455.1_ASM480145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801455.1_ASM480145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:27,146] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:27,162] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:27,163] [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_009720625.1	s__Metabacillus sp004801455	99.9956	1796	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017497975.1	s__Metabacillus sp017497975	80.8841	860	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217835.1	s__Metabacillus litoralis_A	80.6126	837	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_003259415.1	s__Metabacillus sp003259415	80.2433	735	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981385.1	s__Metabacillus sp000981385	79.9961	708	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	79.1252	453	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_000518865.1	s__Metabacillus sp000518865	78.9926	460	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908395.1	s__Metabacillus crassostreae	78.8505	478	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994985.1	s__Metabacillus litoralis	78.7392	492	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866655.1	s__Neobacillus sp001866655	77.7609	179	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	77.1343	148	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	77.03	149	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:27,165] [INFO] GTDB search result was written to GCF_004801455.1_ASM480145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:27,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:27,171] [INFO] DFAST_QC result json was written to GCF_004801455.1_ASM480145v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:27,171] [INFO] DFAST_QC completed!
[2024-01-24 12:43:27,172] [INFO] Total running time: 0h1m18s