[2024-01-24 12:21:36,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference
[2024-01-24 12:21:37,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,383] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg19468a5d-4435-4be0-8ab0-b436fef0fb69/GCF_007559425.1_ASM755942v1_genomic.fna.gz | prodigal -d GCF_007559425.1_ASM755942v1_genomic.fna/cds.fna -a GCF_007559425.1_ASM755942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:42,974] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:42,974] [INFO] Task started: HMMsearch
[2024-01-24 12:21:42,975] [INFO] Running command: hmmsearch --tblout GCF_007559425.1_ASM755942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference/reference_markers.hmm GCF_007559425.1_ASM755942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:43,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:43,221] [INFO] Found 6/6 markers.
[2024-01-24 12:21:43,250] [INFO] Query marker FASTA was written to GCF_007559425.1_ASM755942v1_genomic.fna/markers.fasta
[2024-01-24 12:21:43,250] [INFO] Task started: Blastn
[2024-01-24 12:21:43,251] [INFO] Running command: blastn -query GCF_007559425.1_ASM755942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference/reference_markers.fasta -out GCF_007559425.1_ASM755942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:43,836] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:43,841] [INFO] Selected 15 target genomes.
[2024-01-24 12:21:43,842] [INFO] Target genome list was writen to GCF_007559425.1_ASM755942v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:43,894] [INFO] Task started: fastANI
[2024-01-24 12:21:43,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg19468a5d-4435-4be0-8ab0-b436fef0fb69/GCF_007559425.1_ASM755942v1_genomic.fna.gz --refList GCF_007559425.1_ASM755942v1_genomic.fna/target_genomes.txt --output GCF_007559425.1_ASM755942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:52,540] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:52,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:52,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:52,550] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:21:52,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:52,551] [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
Allobacillus salarius	strain=SKP4-8	GCA_007559425.1	1955272	1955272	type	True	99.9999	818	819	95	conclusive
Allobacillus saliphilus	strain=SKP8-2	GCA_018138385.1	2912308	2912308	type	True	94.2795	705	819	95	below_threshold
Allobacillus halotolerans	strain=LMG 24826	GCA_018967645.1	570278	570278	type	True	87.2985	689	819	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.605	52	819	95	below_threshold
Alkalibacillus aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	76.9253	82	819	95	below_threshold
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	76.5413	85	819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:52,552] [INFO] DFAST Taxonomy check result was written to GCF_007559425.1_ASM755942v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:52,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:52,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:52,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference/checkm_data
[2024-01-24 12:21:52,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:52,580] [INFO] Task started: CheckM
[2024-01-24 12:21:52,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007559425.1_ASM755942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007559425.1_ASM755942v1_genomic.fna/checkm_input GCF_007559425.1_ASM755942v1_genomic.fna/checkm_result
[2024-01-24 12:22:16,403] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:16,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:16,429] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:16,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:16,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007559425.1_ASM755942v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:16,431] [INFO] Task started: Blastn
[2024-01-24 12:22:16,431] [INFO] Running command: blastn -query GCF_007559425.1_ASM755942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74255b9f-599b-438c-bc48-eb8f66cc08e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007559425.1_ASM755942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:17,197] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:17,202] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:17,202] [INFO] Target genome list was writen to GCF_007559425.1_ASM755942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:17,245] [INFO] Task started: fastANI
[2024-01-24 12:22:17,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg19468a5d-4435-4be0-8ab0-b436fef0fb69/GCF_007559425.1_ASM755942v1_genomic.fna.gz --refList GCF_007559425.1_ASM755942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007559425.1_ASM755942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:26,093] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,100] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:26,100] [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_007559425.1	s__Allobacillus sp007559425	99.9999	818	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018138385.1	s__Allobacillus sp018138385	94.2834	704	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967645.1	s__Allobacillus halotolerans	87.2985	689	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	97.75	97.75	0.93	0.93	2	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	77.5438	53	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000269905.1	s__Alkalibacillus haloalkaliphilus_A	76.9597	84	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595945.1	s__Alkalibacillus sp014595945	76.9253	82	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	76.5413	85	819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,101] [INFO] GTDB search result was written to GCF_007559425.1_ASM755942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:26,102] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:26,105] [INFO] DFAST_QC result json was written to GCF_007559425.1_ASM755942v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:26,105] [INFO] DFAST_QC completed!
[2024-01-24 12:22:26,105] [INFO] Total running time: 0h0m50s