[2024-01-25 18:00:20,629] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference
[2024-01-25 18:00:21,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:21,754] [INFO] Task started: Prodigal
[2024-01-25 18:00:21,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg452440a4-61a1-4a56-b160-5d1be195c2d6/GCF_014647315.1_ASM1464731v1_genomic.fna.gz | prodigal -d GCF_014647315.1_ASM1464731v1_genomic.fna/cds.fna -a GCF_014647315.1_ASM1464731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:29,930] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:29,930] [INFO] Task started: HMMsearch
[2024-01-25 18:00:29,930] [INFO] Running command: hmmsearch --tblout GCF_014647315.1_ASM1464731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference/reference_markers.hmm GCF_014647315.1_ASM1464731v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:30,120] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:30,121] [INFO] Found 6/6 markers.
[2024-01-25 18:00:30,146] [INFO] Query marker FASTA was written to GCF_014647315.1_ASM1464731v1_genomic.fna/markers.fasta
[2024-01-25 18:00:30,146] [INFO] Task started: Blastn
[2024-01-25 18:00:30,146] [INFO] Running command: blastn -query GCF_014647315.1_ASM1464731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference/reference_markers.fasta -out GCF_014647315.1_ASM1464731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:30,735] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:30,738] [INFO] Selected 13 target genomes.
[2024-01-25 18:00:30,738] [INFO] Target genome list was writen to GCF_014647315.1_ASM1464731v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:30,752] [INFO] Task started: fastANI
[2024-01-25 18:00:30,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg452440a4-61a1-4a56-b160-5d1be195c2d6/GCF_014647315.1_ASM1464731v1_genomic.fna.gz --refList GCF_014647315.1_ASM1464731v1_genomic.fna/target_genomes.txt --output GCF_014647315.1_ASM1464731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:37,724] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:37,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:37,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:37,733] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:00:37,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:37,733] [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 cellulosilyticus	strain=JCM 18487	GCA_014647315.1	1003997	1003997	type	True	100.0	835	840	95	conclusive
Alicyclobacillus cellulosilyticus	strain=Sueoka	GCA_020521335.1	1003997	1003997	type	True	99.9288	804	840	95	conclusive
Alicyclobacillus macrosporangiidus	strain=DSM 17980	GCA_900116805.1	392015	392015	type	True	77.9804	174	840	95	below_threshold
Alicyclobacillus acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	77.3706	102	840	95	below_threshold
Alicyclobacillus kakegawensis	strain=NBRC 103104	GCA_001552655.1	392012	392012	type	True	77.1752	123	840	95	below_threshold
Alicyclobacillus shizuokensis	strain=NBRC 103103	GCA_001552255.1	392014	392014	type	True	77.0534	117	840	95	below_threshold
Alicyclobacillus mali	strain=FSL-W10-0018	GCA_017329565.1	1123961	1123961	type	True	76.8825	104	840	95	below_threshold
Calditerricola satsumensis	strain=JCM 14719	GCA_014646935.1	373054	373054	type	True	76.6203	60	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:37,735] [INFO] DFAST Taxonomy check result was written to GCF_014647315.1_ASM1464731v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:37,735] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:37,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:37,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference/checkm_data
[2024-01-25 18:00:37,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:37,764] [INFO] Task started: CheckM
[2024-01-25 18:00:37,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647315.1_ASM1464731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647315.1_ASM1464731v1_genomic.fna/checkm_input GCF_014647315.1_ASM1464731v1_genomic.fna/checkm_result
[2024-01-25 18:01:12,417] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:12,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:12,430] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:12,431] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:12,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647315.1_ASM1464731v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:12,431] [INFO] Task started: Blastn
[2024-01-25 18:01:12,431] [INFO] Running command: blastn -query GCF_014647315.1_ASM1464731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e7d2dfb-23a1-47be-ad88-0a9770048227/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647315.1_ASM1464731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:13,337] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:13,340] [INFO] Selected 17 target genomes.
[2024-01-25 18:01:13,340] [INFO] Target genome list was writen to GCF_014647315.1_ASM1464731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:13,353] [INFO] Task started: fastANI
[2024-01-25 18:01:13,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg452440a4-61a1-4a56-b160-5d1be195c2d6/GCF_014647315.1_ASM1464731v1_genomic.fna.gz --refList GCF_014647315.1_ASM1464731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647315.1_ASM1464731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:23,018] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:23,031] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:23,032] [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_014647315.1	s__Alicyclobacillus_J cellulosilyticus	100.0	835	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_J	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900116805.1	s__Alicyclobacillus_H macrosporangiidus	77.9725	175	840	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_000702485.1	s__Alicyclobacillus_H macrosporangiidus_B	77.8883	171	840	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_000024285.1	s__Alicyclobacillus acidocaldarius	77.3706	102	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570745.1	s__Alicyclobacillus mali	77.1938	106	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.73	98.27	0.95	0.93	4	-
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	77.1118	102	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552255.1	s__Alicyclobacillus_G shizuokensis	77.0764	116	840	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_000430585.1	s__Alicyclobacillus_G herbarius	77.0567	78	840	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_001552675.1	s__Alicyclobacillus sendaiensis	76.8899	101	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646935.1	s__Calditerricola satsumensis	76.6203	60	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Calditerricolales;f__Calditerricolaceae;g__Calditerricola	95.0	99.92	99.92	0.99	0.99	2	-
GCA_002159085.1	s__Thermobacillus sp002159085	75.7289	56	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:23,033] [INFO] GTDB search result was written to GCF_014647315.1_ASM1464731v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:23,034] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:23,037] [INFO] DFAST_QC result json was written to GCF_014647315.1_ASM1464731v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:23,038] [INFO] DFAST_QC completed!
[2024-01-25 18:01:23,038] [INFO] Total running time: 0h1m2s