[2024-01-25 18:44:35,593] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:35,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:35,594] [INFO] DQC Reference Directory: /var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference
[2024-01-25 18:44:36,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:36,728] [INFO] Task started: Prodigal
[2024-01-25 18:44:36,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f506c46-d465-4086-861a-35f926faa441/GCF_028751525.1_ASM2875152v1_genomic.fna.gz | prodigal -d GCF_028751525.1_ASM2875152v1_genomic.fna/cds.fna -a GCF_028751525.1_ASM2875152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:47,516] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:47,516] [INFO] Task started: HMMsearch
[2024-01-25 18:44:47,516] [INFO] Running command: hmmsearch --tblout GCF_028751525.1_ASM2875152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference/reference_markers.hmm GCF_028751525.1_ASM2875152v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:47,739] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:47,740] [INFO] Found 6/6 markers.
[2024-01-25 18:44:47,770] [INFO] Query marker FASTA was written to GCF_028751525.1_ASM2875152v1_genomic.fna/markers.fasta
[2024-01-25 18:44:47,770] [INFO] Task started: Blastn
[2024-01-25 18:44:47,770] [INFO] Running command: blastn -query GCF_028751525.1_ASM2875152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference/reference_markers.fasta -out GCF_028751525.1_ASM2875152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:48,353] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:48,358] [INFO] Selected 22 target genomes.
[2024-01-25 18:44:48,359] [INFO] Target genome list was writen to GCF_028751525.1_ASM2875152v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:48,372] [INFO] Task started: fastANI
[2024-01-25 18:44:48,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f506c46-d465-4086-861a-35f926faa441/GCF_028751525.1_ASM2875152v1_genomic.fna.gz --refList GCF_028751525.1_ASM2875152v1_genomic.fna/target_genomes.txt --output GCF_028751525.1_ASM2875152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:02,309] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:02,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:02,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:02,318] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:02,318] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:02,318] [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
Alicyclobacillus acidoterrestris	strain=DSM 3922	GCA_022674245.1	1450	1450	type	True	79.9633	87	1205	95	below_threshold
Alicyclobacillus suci	strain=VF-FSL-W10-0049	GCA_017329615.1	2816080	2816080	type	True	79.0537	65	1205	95	below_threshold
Alicyclobacillus contaminans	strain=DSM 17975	GCA_000429525.1	392016	392016	type	True	78.1184	93	1205	95	below_threshold
Alicyclobacillus acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	78.0349	71	1205	95	below_threshold
Alicyclobacillus acidoterrestris	strain=ATCC 49025	GCA_000444055.1	1450	1450	type	True	77.6241	67	1205	95	below_threshold
Alicyclobacillus herbarius	strain=DSM 13609	GCA_000430585.1	122960	122960	type	True	77.2862	67	1205	95	below_threshold
Alicyclobacillus shizuokensis	strain=NBRC 103103	GCA_001552255.1	392014	392014	type	True	77.2247	81	1205	95	below_threshold
Alicyclobacillus cellulosilyticus	strain=JCM 18487	GCA_014647315.1	1003997	1003997	type	True	77.0899	87	1205	95	below_threshold
Alicyclobacillus cellulosilyticus	strain=Sueoka	GCA_020521335.1	1003997	1003997	type	True	76.8887	91	1205	95	below_threshold
Alicyclobacillus macrosporangiidus	strain=DSM 17980	GCA_900116805.1	392015	392015	type	True	76.7749	102	1205	95	below_threshold
Alicyclobacillus mali	strain=FSL-W10-0018	GCA_017329565.1	1123961	1123961	type	True	76.7146	54	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:02,319] [INFO] DFAST Taxonomy check result was written to GCF_028751525.1_ASM2875152v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:02,320] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:02,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:02,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference/checkm_data
[2024-01-25 18:45:02,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:02,358] [INFO] Task started: CheckM
[2024-01-25 18:45:02,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028751525.1_ASM2875152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028751525.1_ASM2875152v1_genomic.fna/checkm_input GCF_028751525.1_ASM2875152v1_genomic.fna/checkm_result
[2024-01-25 18:45:37,070] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:37,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:37,108] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:37,108] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:37,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028751525.1_ASM2875152v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:37,109] [INFO] Task started: Blastn
[2024-01-25 18:45:37,109] [INFO] Running command: blastn -query GCF_028751525.1_ASM2875152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16ef219-8a06-4378-8753-32892a7e2d11/dqc_reference/reference_markers_gtdb.fasta -out GCF_028751525.1_ASM2875152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:37,976] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:37,979] [INFO] Selected 29 target genomes.
[2024-01-25 18:45:37,979] [INFO] Target genome list was writen to GCF_028751525.1_ASM2875152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:38,033] [INFO] Task started: fastANI
[2024-01-25 18:45:38,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f506c46-d465-4086-861a-35f926faa441/GCF_028751525.1_ASM2875152v1_genomic.fna.gz --refList GCF_028751525.1_ASM2875152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028751525.1_ASM2875152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:55,011] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:55,020] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:45:55,020] [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_000024285.1	s__Alicyclobacillus acidocaldarius	78.4721	72	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702485.1	s__Alicyclobacillus_H macrosporangiidus_B	78.2752	122	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429525.1	s__Alicyclobacillus_A contaminans	78.0649	92	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991715.1	s__Alicyclobacillus acidoterrestris_A	77.7966	60	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.33	97.80	0.90	0.90	3	-
GCF_000444055.1	s__Alicyclobacillus acidoterrestris	77.6162	70	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430585.1	s__Alicyclobacillus_G herbarius	77.2855	67	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552255.1	s__Alicyclobacillus_G shizuokensis	77.2247	81	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	77.1288	65	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647315.1	s__Alicyclobacillus_J cellulosilyticus	77.0899	87	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570745.1	s__Alicyclobacillus mali	76.8743	50	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.73	98.27	0.95	0.93	4	-
GCF_900116805.1	s__Alicyclobacillus_H macrosporangiidus	76.838	104	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017329635.1	s__Alicyclobacillus sp017329635	76.5427	53	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:55,023] [INFO] GTDB search result was written to GCF_028751525.1_ASM2875152v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:55,023] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:55,026] [INFO] DFAST_QC result json was written to GCF_028751525.1_ASM2875152v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:55,026] [INFO] DFAST_QC completed!
[2024-01-25 18:45:55,026] [INFO] Total running time: 0h1m19s