[2024-01-24 12:36:24,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference
[2024-01-24 12:36:26,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,222] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgf889461a-aed2-47ca-9b78-9c92b2369a88/GCF_002003465.1_B157_assembly01_genomic.fna.gz | prodigal -d GCF_002003465.1_B157_assembly01_genomic.fna/cds.fna -a GCF_002003465.1_B157_assembly01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:35,461] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:35,461] [INFO] Task started: HMMsearch
[2024-01-24 12:36:35,461] [INFO] Running command: hmmsearch --tblout GCF_002003465.1_B157_assembly01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference/reference_markers.hmm GCF_002003465.1_B157_assembly01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:35,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:35,715] [INFO] Found 6/6 markers.
[2024-01-24 12:36:35,748] [INFO] Query marker FASTA was written to GCF_002003465.1_B157_assembly01_genomic.fna/markers.fasta
[2024-01-24 12:36:35,749] [INFO] Task started: Blastn
[2024-01-24 12:36:35,749] [INFO] Running command: blastn -query GCF_002003465.1_B157_assembly01_genomic.fna/markers.fasta -db /var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference/reference_markers.fasta -out GCF_002003465.1_B157_assembly01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:36,368] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:36,371] [INFO] Selected 24 target genomes.
[2024-01-24 12:36:36,372] [INFO] Target genome list was writen to GCF_002003465.1_B157_assembly01_genomic.fna/target_genomes.txt
[2024-01-24 12:36:36,386] [INFO] Task started: fastANI
[2024-01-24 12:36:36,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgf889461a-aed2-47ca-9b78-9c92b2369a88/GCF_002003465.1_B157_assembly01_genomic.fna.gz --refList GCF_002003465.1_B157_assembly01_genomic.fna/target_genomes.txt --output GCF_002003465.1_B157_assembly01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:54,561] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:54,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:54,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:54,567] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:54,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:54,567] [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
Caenibacillus caldisaponilyticus	strain=B157	GCA_002003465.1	1674942	1674942	type	True	100.0	1019	1030	95	conclusive
Caldibacillus debilis	strain=DSM 16016	GCA_000383875.1	301148	301148	type	True	78.7936	72	1030	95	below_threshold
Geobacillus icigianus	strain=G1w1	GCA_000750005.1	1430331	1430331	type	True	76.7666	78	1030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:54,569] [INFO] DFAST Taxonomy check result was written to GCF_002003465.1_B157_assembly01_genomic.fna/tc_result.tsv
[2024-01-24 12:36:54,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:54,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:54,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference/checkm_data
[2024-01-24 12:36:54,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:54,606] [INFO] Task started: CheckM
[2024-01-24 12:36:54,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002003465.1_B157_assembly01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002003465.1_B157_assembly01_genomic.fna/checkm_input GCF_002003465.1_B157_assembly01_genomic.fna/checkm_result
[2024-01-24 12:37:25,995] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:25,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:26,022] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:26,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:26,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002003465.1_B157_assembly01_genomic.fna/markers.fasta)
[2024-01-24 12:37:26,024] [INFO] Task started: Blastn
[2024-01-24 12:37:26,024] [INFO] Running command: blastn -query GCF_002003465.1_B157_assembly01_genomic.fna/markers.fasta -db /var/lib/cwl/stg55962efe-fb29-4a49-a2e5-b95e905303b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002003465.1_B157_assembly01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:26,859] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:26,863] [INFO] Selected 23 target genomes.
[2024-01-24 12:37:26,863] [INFO] Target genome list was writen to GCF_002003465.1_B157_assembly01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:26,889] [INFO] Task started: fastANI
[2024-01-24 12:37:26,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgf889461a-aed2-47ca-9b78-9c92b2369a88/GCF_002003465.1_B157_assembly01_genomic.fna.gz --refList GCF_002003465.1_B157_assembly01_genomic.fna/target_genomes_gtdb.txt --output GCF_002003465.1_B157_assembly01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:40,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:40,776] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:40,776] [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_002003465.1	s__Caenibacillus caldisaponilyticus	100.0	1019	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Caenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000383875.1	s__Caldibacillus debilis	78.7419	73	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Caldibacillus	95.0	98.65	98.42	0.94	0.89	8	-
GCF_001544135.1	s__Geobacillus zalihae	77.0469	83	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	97.99	97.08	0.88	0.86	9	-
GCF_000750005.1	s__Geobacillus icigianus	76.7666	78	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	97.70	96.51	0.91	0.84	5	-
GCA_001610955.1	s__Geobacillus thermoleovorans	76.7162	81	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	98.02	96.77	0.87	0.82	28	-
GCF_001908025.1	s__Geobacillus proteiniphilus	76.2819	91	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9151	98.36	98.36	0.87	0.87	2	-
GCF_002809955.1	s__Geobacillus sp002809955	76.1374	73	1030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.916	97.67	97.25	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:40,778] [INFO] GTDB search result was written to GCF_002003465.1_B157_assembly01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:40,780] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:40,783] [INFO] DFAST_QC result json was written to GCF_002003465.1_B157_assembly01_genomic.fna/dqc_result.json
[2024-01-24 12:37:40,784] [INFO] DFAST_QC completed!
[2024-01-24 12:37:40,784] [INFO] Total running time: 0h1m16s