[2024-01-25 18:46:20,530] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:20,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:20,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference
[2024-01-25 18:46:21,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:21,635] [INFO] Task started: Prodigal
[2024-01-25 18:46:21,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgc12643b1-d1d6-40e5-93dd-ddbd46169985/GCF_002217735.1_ASM221773v1_genomic.fna.gz | prodigal -d GCF_002217735.1_ASM221773v1_genomic.fna/cds.fna -a GCF_002217735.1_ASM221773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:30,098] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:30,098] [INFO] Task started: HMMsearch
[2024-01-25 18:46:30,098] [INFO] Running command: hmmsearch --tblout GCF_002217735.1_ASM221773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference/reference_markers.hmm GCF_002217735.1_ASM221773v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:30,329] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:30,330] [INFO] Found 6/6 markers.
[2024-01-25 18:46:30,361] [INFO] Query marker FASTA was written to GCF_002217735.1_ASM221773v1_genomic.fna/markers.fasta
[2024-01-25 18:46:30,361] [INFO] Task started: Blastn
[2024-01-25 18:46:30,361] [INFO] Running command: blastn -query GCF_002217735.1_ASM221773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference/reference_markers.fasta -out GCF_002217735.1_ASM221773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:30,919] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:30,922] [INFO] Selected 18 target genomes.
[2024-01-25 18:46:30,922] [INFO] Target genome list was writen to GCF_002217735.1_ASM221773v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:30,936] [INFO] Task started: fastANI
[2024-01-25 18:46:30,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgc12643b1-d1d6-40e5-93dd-ddbd46169985/GCF_002217735.1_ASM221773v1_genomic.fna.gz --refList GCF_002217735.1_ASM221773v1_genomic.fna/target_genomes.txt --output GCF_002217735.1_ASM221773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:43,536] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:43,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:43,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:43,544] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:46:43,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:43,544] [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
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	98.35	934	1262	95	conclusive
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	98.3	937	1262	95	conclusive
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	98.2256	957	1262	95	conclusive
Parageobacillus thermantarcticus	strain=M1	GCA_900111865.1	186116	186116	type	True	86.0993	816	1262	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	85.4428	881	1262	95	below_threshold
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	85.4265	894	1262	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=DSM 12041	GCA_014196025.1	81408	81408	type	True	85.0818	816	1262	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	85.01	801	1262	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	78.0111	231	1262	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.6524	67	1262	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.3674	75	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:43,546] [INFO] DFAST Taxonomy check result was written to GCF_002217735.1_ASM221773v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:43,546] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:43,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:43,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference/checkm_data
[2024-01-25 18:46:43,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:43,586] [INFO] Task started: CheckM
[2024-01-25 18:46:43,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217735.1_ASM221773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217735.1_ASM221773v1_genomic.fna/checkm_input GCF_002217735.1_ASM221773v1_genomic.fna/checkm_result
[2024-01-25 18:47:12,416] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:12,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:12,436] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:12,437] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:12,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217735.1_ASM221773v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:12,437] [INFO] Task started: Blastn
[2024-01-25 18:47:12,437] [INFO] Running command: blastn -query GCF_002217735.1_ASM221773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebffa3a-ab50-4a1d-b232-49b315875870/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217735.1_ASM221773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:13,238] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:13,241] [INFO] Selected 12 target genomes.
[2024-01-25 18:47:13,241] [INFO] Target genome list was writen to GCF_002217735.1_ASM221773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:13,253] [INFO] Task started: fastANI
[2024-01-25 18:47:13,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgc12643b1-d1d6-40e5-93dd-ddbd46169985/GCF_002217735.1_ASM221773v1_genomic.fna.gz --refList GCF_002217735.1_ASM221773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217735.1_ASM221773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:22,684] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:22,689] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:22,690] [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_003688615.2	s__Parageobacillus toebii	98.2274	956	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	conclusive
GCF_900111865.1	s__Parageobacillus thermantarcticus	86.0887	817	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	85.8074	877	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	85.4174	886	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_000632515.1	s__Saccharococcus sp000632515	85.3709	828	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761475.1	s__Saccharococcus thermophilus	85.0282	786	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632715.1	s__Saccharococcus caldoxylosilyticus	85.0269	800	1262	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:22,692] [INFO] GTDB search result was written to GCF_002217735.1_ASM221773v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:22,692] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:22,695] [INFO] DFAST_QC result json was written to GCF_002217735.1_ASM221773v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:22,695] [INFO] DFAST_QC completed!
[2024-01-25 18:47:22,695] [INFO] Total running time: 0h1m2s