[2024-01-24 12:22:28,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference
[2024-01-24 12:22:29,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,976] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,976] [INFO] Running command: gunzip -c /var/lib/cwl/stga6a0bf0f-850e-4429-af58-1cd2694ba4e2/GCF_006539965.1_ASM653996v1_genomic.fna.gz | prodigal -d GCF_006539965.1_ASM653996v1_genomic.fna/cds.fna -a GCF_006539965.1_ASM653996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:43,584] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:43,584] [INFO] Task started: HMMsearch
[2024-01-24 12:22:43,584] [INFO] Running command: hmmsearch --tblout GCF_006539965.1_ASM653996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference/reference_markers.hmm GCF_006539965.1_ASM653996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:43,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:43,960] [INFO] Found 6/6 markers.
[2024-01-24 12:22:44,017] [INFO] Query marker FASTA was written to GCF_006539965.1_ASM653996v1_genomic.fna/markers.fasta
[2024-01-24 12:22:44,017] [INFO] Task started: Blastn
[2024-01-24 12:22:44,017] [INFO] Running command: blastn -query GCF_006539965.1_ASM653996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference/reference_markers.fasta -out GCF_006539965.1_ASM653996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:44,664] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:44,669] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:44,670] [INFO] Target genome list was writen to GCF_006539965.1_ASM653996v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:44,674] [INFO] Task started: fastANI
[2024-01-24 12:22:44,674] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a0bf0f-850e-4429-af58-1cd2694ba4e2/GCF_006539965.1_ASM653996v1_genomic.fna.gz --refList GCF_006539965.1_ASM653996v1_genomic.fna/target_genomes.txt --output GCF_006539965.1_ASM653996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:54,977] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:54,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:54,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:54,984] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:22:54,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:54,985] [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
Aneurinibacillus migulanus	strain=NBRC 15520	GCA_006539965.1	47500	47500	type	True	100.0	1818	1826	95	conclusive
Aneurinibacillus migulanus	strain=DSM 2895	GCA_900100065.1	47500	47500	type	True	99.9978	1824	1826	95	conclusive
Aneurinibacillus migulanus	strain=NCTC 7096	GCA_000878905.1	47500	47500	type	True	99.9966	1825	1826	95	conclusive
Aneurinibacillus migulanus	strain=DSM 2895	GCA_001274715.1	47500	47500	type	True	99.9921	1825	1826	95	conclusive
Aneurinibacillus aneurinilyticus	strain=ATCC 12856	GCA_000466385.1	1391	1391	type	True	87.3035	1238	1826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:54,987] [INFO] DFAST Taxonomy check result was written to GCF_006539965.1_ASM653996v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:54,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:54,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:54,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference/checkm_data
[2024-01-24 12:22:54,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:55,052] [INFO] Task started: CheckM
[2024-01-24 12:22:55,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539965.1_ASM653996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539965.1_ASM653996v1_genomic.fna/checkm_input GCF_006539965.1_ASM653996v1_genomic.fna/checkm_result
[2024-01-24 12:23:39,737] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:39,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:39,771] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:39,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:39,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539965.1_ASM653996v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:39,772] [INFO] Task started: Blastn
[2024-01-24 12:23:39,773] [INFO] Running command: blastn -query GCF_006539965.1_ASM653996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50db1cc6-2640-441c-b3e0-44be0dc7c5cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539965.1_ASM653996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:40,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:40,532] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:40,532] [INFO] Target genome list was writen to GCF_006539965.1_ASM653996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:40,556] [INFO] Task started: fastANI
[2024-01-24 12:23:40,556] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a0bf0f-850e-4429-af58-1cd2694ba4e2/GCF_006539965.1_ASM653996v1_genomic.fna.gz --refList GCF_006539965.1_ASM653996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539965.1_ASM653996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:53,365] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:53,375] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:53,375] [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_001274715.1	s__Aneurinibacillus migulanus	99.9921	1825	1826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.46	98.76	0.96	0.91	8	conclusive
GCF_000466385.1	s__Aneurinibacillus aneurinilyticus	87.2959	1239	1826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.57	99.14	0.94	0.88	3	-
GCF_007991215.1	s__Aneurinibacillus danicus	79.4392	532	1826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.16	99.16	0.84	0.84	2	-
GCF_900099925.1	s__Aneurinibacillus thermoaerophilus	78.0632	334	1826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.68	99.68	0.95	0.95	2	-
GCF_001015055.1	s__Aneurinibacillus_A tyrosinisolvens	77.4808	177	1826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:53,377] [INFO] GTDB search result was written to GCF_006539965.1_ASM653996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:53,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:53,396] [INFO] DFAST_QC result json was written to GCF_006539965.1_ASM653996v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:53,396] [INFO] DFAST_QC completed!
[2024-01-24 12:23:53,397] [INFO] Total running time: 0h1m25s