[2024-01-24 15:10:54,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,141] [INFO] DQC Reference Directory: /var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference
[2024-01-24 15:10:56,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,634] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg95fa863f-8258-4fd0-a4c3-d67654375a39/GCF_004366795.1_ASM436679v1_genomic.fna.gz | prodigal -d GCF_004366795.1_ASM436679v1_genomic.fna/cds.fna -a GCF_004366795.1_ASM436679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:06,676] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:06,676] [INFO] Task started: HMMsearch
[2024-01-24 15:11:06,676] [INFO] Running command: hmmsearch --tblout GCF_004366795.1_ASM436679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference/reference_markers.hmm GCF_004366795.1_ASM436679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:06,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:06,960] [INFO] Found 6/6 markers.
[2024-01-24 15:11:07,001] [INFO] Query marker FASTA was written to GCF_004366795.1_ASM436679v1_genomic.fna/markers.fasta
[2024-01-24 15:11:07,001] [INFO] Task started: Blastn
[2024-01-24 15:11:07,002] [INFO] Running command: blastn -query GCF_004366795.1_ASM436679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference/reference_markers.fasta -out GCF_004366795.1_ASM436679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:07,709] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:07,712] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:07,713] [INFO] Target genome list was writen to GCF_004366795.1_ASM436679v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:07,747] [INFO] Task started: fastANI
[2024-01-24 15:11:07,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg95fa863f-8258-4fd0-a4c3-d67654375a39/GCF_004366795.1_ASM436679v1_genomic.fna.gz --refList GCF_004366795.1_ASM436679v1_genomic.fna/target_genomes.txt --output GCF_004366795.1_ASM436679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:15,706] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:15,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:15,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:15,712] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:15,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:15,713] [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 sacchari	strain=DSM 17974	GCA_004366795.1	392010	392010	type	True	100.0	947	951	95	conclusive
Alicyclobacillus hesperidum	strain=DSM 12489	GCA_900107035.1	89784	89784	type	True	83.6518	754	951	95	below_threshold
Alicyclobacillus vulcanalis	strain=DSM 16176	GCA_900156755.1	252246	252246	type	True	78.0157	133	951	95	below_threshold
Alicyclobacillus sendaiensis	strain=NBRC 100866	GCA_001552675.1	192387	192387	type	True	77.2058	103	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:15,714] [INFO] DFAST Taxonomy check result was written to GCF_004366795.1_ASM436679v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:15,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:15,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:15,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference/checkm_data
[2024-01-24 15:11:15,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:15,752] [INFO] Task started: CheckM
[2024-01-24 15:11:15,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366795.1_ASM436679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366795.1_ASM436679v1_genomic.fna/checkm_input GCF_004366795.1_ASM436679v1_genomic.fna/checkm_result
[2024-01-24 15:11:49,970] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:49,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:49,993] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:49,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:49,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366795.1_ASM436679v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:49,995] [INFO] Task started: Blastn
[2024-01-24 15:11:49,995] [INFO] Running command: blastn -query GCF_004366795.1_ASM436679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca240c14-c9fa-4f62-997a-05fe5fc86262/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366795.1_ASM436679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:50,839] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:50,842] [INFO] Selected 9 target genomes.
[2024-01-24 15:11:50,842] [INFO] Target genome list was writen to GCF_004366795.1_ASM436679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:50,850] [INFO] Task started: fastANI
[2024-01-24 15:11:50,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg95fa863f-8258-4fd0-a4c3-d67654375a39/GCF_004366795.1_ASM436679v1_genomic.fna.gz --refList GCF_004366795.1_ASM436679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366795.1_ASM436679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:55,890] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:55,902] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:55,902] [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_004366795.1	s__Alicyclobacillus sacchari	100.0	946	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001447355.1	s__Alicyclobacillus tengchongensis	83.6584	733	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	N/A	N/A	N/A	N/A	1	-
GCF_900107035.1	s__Alicyclobacillus hesperidum	83.6518	754	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	98.78	98.78	0.94	0.94	2	-
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	78.7493	137	951	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	77.9598	131	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219875.1	s__Alicyclobacillus acidocaldarius_A	77.4181	110	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552675.1	s__Alicyclobacillus sendaiensis	77.191	102	951	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 15:11:55,904] [INFO] GTDB search result was written to GCF_004366795.1_ASM436679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:55,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:55,908] [INFO] DFAST_QC result json was written to GCF_004366795.1_ASM436679v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:55,908] [INFO] DFAST_QC completed!
[2024-01-24 15:11:55,908] [INFO] Total running time: 0h1m2s