[2024-01-24 15:26:54,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference
[2024-01-24 15:26:56,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,309] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg424111a9-f803-493d-a78a-42c435810411/GCF_001552255.1_ASM155225v1_genomic.fna.gz | prodigal -d GCF_001552255.1_ASM155225v1_genomic.fna/cds.fna -a GCF_001552255.1_ASM155225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,184] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,184] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,184] [INFO] Running command: hmmsearch --tblout GCF_001552255.1_ASM155225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference/reference_markers.hmm GCF_001552255.1_ASM155225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:08,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:08,417] [INFO] Found 6/6 markers.
[2024-01-24 15:27:08,447] [INFO] Query marker FASTA was written to GCF_001552255.1_ASM155225v1_genomic.fna/markers.fasta
[2024-01-24 15:27:08,448] [INFO] Task started: Blastn
[2024-01-24 15:27:08,448] [INFO] Running command: blastn -query GCF_001552255.1_ASM155225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference/reference_markers.fasta -out GCF_001552255.1_ASM155225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:09,043] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:09,047] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:09,048] [INFO] Target genome list was writen to GCF_001552255.1_ASM155225v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:09,055] [INFO] Task started: fastANI
[2024-01-24 15:27:09,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg424111a9-f803-493d-a78a-42c435810411/GCF_001552255.1_ASM155225v1_genomic.fna.gz --refList GCF_001552255.1_ASM155225v1_genomic.fna/target_genomes.txt --output GCF_001552255.1_ASM155225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:22,656] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:22,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:22,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:22,666] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:22,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:22,666] [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 shizuokensis	strain=NBRC 103103	GCA_001552255.1	392014	392014	type	True	100.0	1134	1139	95	conclusive
Alicyclobacillus kakegawensis	strain=NBRC 103104	GCA_001552655.1	392012	392012	type	True	91.8247	890	1139	95	below_threshold
Alicyclobacillus herbarius	strain=DSM 13609	GCA_000430585.1	122960	122960	type	True	79.1525	401	1139	95	below_threshold
Alicyclobacillus pomorum	strain=DSM 14955	GCA_000472905.1	204470	204470	type	True	77.1193	50	1139	95	below_threshold
Alicyclobacillus cellulosilyticus	strain=JCM 18487	GCA_014647315.1	1003997	1003997	type	True	76.8692	120	1139	95	below_threshold
Alicyclobacillus cellulosilyticus	strain=Sueoka	GCA_020521335.1	1003997	1003997	type	True	76.8664	122	1139	95	below_threshold
Alicyclobacillus fructus	strain=FSL-W10-0059	GCA_017329605.1	2816082	2816082	type	True	76.4853	65	1139	95	below_threshold
Alicyclobacillus vulcanalis	strain=DSM 16176	GCA_900156755.1	252246	252246	type	True	76.3056	66	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:22,668] [INFO] DFAST Taxonomy check result was written to GCF_001552255.1_ASM155225v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:22,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:22,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:22,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference/checkm_data
[2024-01-24 15:27:22,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:22,709] [INFO] Task started: CheckM
[2024-01-24 15:27:22,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552255.1_ASM155225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552255.1_ASM155225v1_genomic.fna/checkm_input GCF_001552255.1_ASM155225v1_genomic.fna/checkm_result
[2024-01-24 15:27:59,823] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:59,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:59,852] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:59,853] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:59,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552255.1_ASM155225v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:59,853] [INFO] Task started: Blastn
[2024-01-24 15:27:59,853] [INFO] Running command: blastn -query GCF_001552255.1_ASM155225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40ee1f43-e19d-46c7-81da-2dbbf496239b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552255.1_ASM155225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:00,754] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:00,758] [INFO] Selected 20 target genomes.
[2024-01-24 15:28:00,758] [INFO] Target genome list was writen to GCF_001552255.1_ASM155225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:00,778] [INFO] Task started: fastANI
[2024-01-24 15:28:00,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg424111a9-f803-493d-a78a-42c435810411/GCF_001552255.1_ASM155225v1_genomic.fna.gz --refList GCF_001552255.1_ASM155225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552255.1_ASM155225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:12,746] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:12,754] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:12,755] [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_001552255.1	s__Alicyclobacillus_G shizuokensis	100.0	1134	1139	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001552655.1	s__Alicyclobacillus_G kakegawensis	91.8431	890	1139	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	79.1525	401	1139	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_900116805.1	s__Alicyclobacillus_H macrosporangiidus	77.6852	139	1139	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_000472905.1	s__Alicyclobacillus_A pomorum	77.1107	51	1139	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_014647315.1	s__Alicyclobacillus_J cellulosilyticus	76.9079	118	1139	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_017329635.1	s__Alicyclobacillus sp017329635	76.4853	65	1139	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000219875.1	s__Alicyclobacillus acidocaldarius_A	76.4126	63	1139	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156755.1	s__Alicyclobacillus vulcanalis	76.3056	66	1139	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:12,756] [INFO] GTDB search result was written to GCF_001552255.1_ASM155225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:12,757] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:12,760] [INFO] DFAST_QC result json was written to GCF_001552255.1_ASM155225v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:12,760] [INFO] DFAST_QC completed!
[2024-01-24 15:28:12,760] [INFO] Total running time: 0h1m18s