[2024-01-24 12:13:42,719] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:42,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:42,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference
[2024-01-24 12:13:44,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:44,091] [INFO] Task started: Prodigal
[2024-01-24 12:13:44,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgb80bbf61-a57b-4f33-bbe8-aaf83fd124fd/GCF_000430625.1_ASM43062v1_genomic.fna.gz | prodigal -d GCF_000430625.1_ASM43062v1_genomic.fna/cds.fna -a GCF_000430625.1_ASM43062v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:54,350] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:54,350] [INFO] Task started: HMMsearch
[2024-01-24 12:13:54,350] [INFO] Running command: hmmsearch --tblout GCF_000430625.1_ASM43062v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference/reference_markers.hmm GCF_000430625.1_ASM43062v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:54,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:54,745] [INFO] Found 6/6 markers.
[2024-01-24 12:13:54,793] [INFO] Query marker FASTA was written to GCF_000430625.1_ASM43062v1_genomic.fna/markers.fasta
[2024-01-24 12:13:54,794] [INFO] Task started: Blastn
[2024-01-24 12:13:54,794] [INFO] Running command: blastn -query GCF_000430625.1_ASM43062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference/reference_markers.fasta -out GCF_000430625.1_ASM43062v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:55,383] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:55,386] [INFO] Selected 23 target genomes.
[2024-01-24 12:13:55,387] [INFO] Target genome list was writen to GCF_000430625.1_ASM43062v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:55,401] [INFO] Task started: fastANI
[2024-01-24 12:13:55,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgb80bbf61-a57b-4f33-bbe8-aaf83fd124fd/GCF_000430625.1_ASM43062v1_genomic.fna.gz --refList GCF_000430625.1_ASM43062v1_genomic.fna/target_genomes.txt --output GCF_000430625.1_ASM43062v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:16,000] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:16,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:16,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:16,010] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:16,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:16,011] [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 terranovensis	strain=DSM 18919	GCA_000430625.1	278991	278991	type	True	100.0	1369	1374	95	conclusive
Aneurinibacillus danicus	strain=NBRC 102444	GCA_007991215.1	267746	267746	type	True	78.5201	149	1374	95	below_threshold
Aneurinibacillus tyrosinisolvens	strain=LL-002	GCA_001015055.1	1443435	1443435	type	True	78.0327	195	1374	95	below_threshold
Aneurinibacillus migulanus	strain=NCTC 7096	GCA_000878905.1	47500	47500	type	True	77.2515	126	1374	95	below_threshold
Aneurinibacillus migulanus	strain=DSM 2895	GCA_001274715.1	47500	47500	type	True	77.2124	130	1374	95	below_threshold
Aneurinibacillus thermoaerophilus	strain=L 420-91	GCA_900099925.1	143495	143495	type	True	77.2081	120	1374	95	below_threshold
Aneurinibacillus aneurinilyticus	strain=ATCC 12856	GCA_000466385.1	1391	1391	type	True	77.0583	109	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:16,013] [INFO] DFAST Taxonomy check result was written to GCF_000430625.1_ASM43062v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:16,014] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:16,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:16,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference/checkm_data
[2024-01-24 12:14:16,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:16,066] [INFO] Task started: CheckM
[2024-01-24 12:14:16,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430625.1_ASM43062v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430625.1_ASM43062v1_genomic.fna/checkm_input GCF_000430625.1_ASM43062v1_genomic.fna/checkm_result
[2024-01-24 12:14:52,554] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:52,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:52,588] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:52,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:52,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430625.1_ASM43062v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:52,589] [INFO] Task started: Blastn
[2024-01-24 12:14:52,589] [INFO] Running command: blastn -query GCF_000430625.1_ASM43062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddd32571-03a8-40fc-8861-ed104e64f5ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430625.1_ASM43062v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:53,372] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:53,376] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:53,377] [INFO] Target genome list was writen to GCF_000430625.1_ASM43062v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:53,398] [INFO] Task started: fastANI
[2024-01-24 12:14:53,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgb80bbf61-a57b-4f33-bbe8-aaf83fd124fd/GCF_000430625.1_ASM43062v1_genomic.fna.gz --refList GCF_000430625.1_ASM43062v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430625.1_ASM43062v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:17,031] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:17,043] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:17,044] [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_000430625.1	s__Aneurinibacillus_B terranovensis	100.0	1369	1374	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007991215.1	s__Aneurinibacillus danicus	78.4925	150	1374	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.16	99.16	0.84	0.84	2	-
GCF_001015055.1	s__Aneurinibacillus_A tyrosinisolvens	78.0176	197	1374	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099925.1	s__Aneurinibacillus thermoaerophilus	77.2125	119	1374	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.68	99.68	0.95	0.95	2	-
GCF_001274715.1	s__Aneurinibacillus migulanus	77.1947	131	1374	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.46	98.76	0.96	0.91	8	-
GCF_000466385.1	s__Aneurinibacillus aneurinilyticus	77.0583	109	1374	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.57	99.14	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:17,046] [INFO] GTDB search result was written to GCF_000430625.1_ASM43062v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:17,046] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:17,049] [INFO] DFAST_QC result json was written to GCF_000430625.1_ASM43062v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:17,049] [INFO] DFAST_QC completed!
[2024-01-24 12:15:17,050] [INFO] Total running time: 0h1m34s