[2024-01-24 13:17:11,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference
[2024-01-24 13:17:12,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,729] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg3061a92c-7e25-4240-81fe-f50fd045386c/GCF_026547205.1_ASM2654720v1_genomic.fna.gz | prodigal -d GCF_026547205.1_ASM2654720v1_genomic.fna/cds.fna -a GCF_026547205.1_ASM2654720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:19,287] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:19,287] [INFO] Task started: HMMsearch
[2024-01-24 13:17:19,288] [INFO] Running command: hmmsearch --tblout GCF_026547205.1_ASM2654720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference/reference_markers.hmm GCF_026547205.1_ASM2654720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:19,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:19,570] [INFO] Found 6/6 markers.
[2024-01-24 13:17:19,598] [INFO] Query marker FASTA was written to GCF_026547205.1_ASM2654720v1_genomic.fna/markers.fasta
[2024-01-24 13:17:19,598] [INFO] Task started: Blastn
[2024-01-24 13:17:19,598] [INFO] Running command: blastn -query GCF_026547205.1_ASM2654720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference/reference_markers.fasta -out GCF_026547205.1_ASM2654720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:20,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:20,176] [INFO] Selected 28 target genomes.
[2024-01-24 13:17:20,177] [INFO] Target genome list was writen to GCF_026547205.1_ASM2654720v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:20,483] [INFO] Task started: fastANI
[2024-01-24 13:17:20,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg3061a92c-7e25-4240-81fe-f50fd045386c/GCF_026547205.1_ASM2654720v1_genomic.fna.gz --refList GCF_026547205.1_ASM2654720v1_genomic.fna/target_genomes.txt --output GCF_026547205.1_ASM2654720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:35,091] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:35,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:35,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:35,102] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:35,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:35,102] [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
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	78.9824	106	979	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	78.5242	58	979	95	below_threshold
Bacillus kwashiorkori	strain=SIT6	GCA_001375515.1	1522318	1522318	type	True	77.8787	81	979	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	77.1186	53	979	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	76.9102	56	979	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.6094	55	979	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:35,104] [INFO] DFAST Taxonomy check result was written to GCF_026547205.1_ASM2654720v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:35,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:35,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:35,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference/checkm_data
[2024-01-24 13:17:35,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:35,138] [INFO] Task started: CheckM
[2024-01-24 13:17:35,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026547205.1_ASM2654720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026547205.1_ASM2654720v1_genomic.fna/checkm_input GCF_026547205.1_ASM2654720v1_genomic.fna/checkm_result
[2024-01-24 13:18:01,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:01,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,336] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:01,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:01,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026547205.1_ASM2654720v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:01,337] [INFO] Task started: Blastn
[2024-01-24 13:18:01,337] [INFO] Running command: blastn -query GCF_026547205.1_ASM2654720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e6c17e8-34ec-4d22-aa34-0f4e2067c279/dqc_reference/reference_markers_gtdb.fasta -out GCF_026547205.1_ASM2654720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:02,151] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:02,155] [INFO] Selected 31 target genomes.
[2024-01-24 13:18:02,155] [INFO] Target genome list was writen to GCF_026547205.1_ASM2654720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:02,231] [INFO] Task started: fastANI
[2024-01-24 13:18:02,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg3061a92c-7e25-4240-81fe-f50fd045386c/GCF_026547205.1_ASM2654720v1_genomic.fna.gz --refList GCF_026547205.1_ASM2654720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026547205.1_ASM2654720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:20,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:20,132] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:20,132] [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_016772275.1	s__Heyndrickxia vini	79.8653	51	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187595.1	s__Anoxybacillus gonensis	79.5668	59	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_003688615.2	s__Parageobacillus toebii	79.1616	60	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_000724485.1	s__Bacillus_Z methanolicus_A	79.0171	62	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001244735.1	s__Bacillus_J andreraoultii	78.7832	105	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_001375515.1	s__Bacillus_BK kwashiorkori	77.8787	81	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_BK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.8681	50	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000836725.1	s__Anoxybacillus thermarum	77.4963	50	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656295.1	s__JACDOC01 sp017656295	76.67	64	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,134] [INFO] GTDB search result was written to GCF_026547205.1_ASM2654720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:20,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:20,137] [INFO] DFAST_QC result json was written to GCF_026547205.1_ASM2654720v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:20,137] [INFO] DFAST_QC completed!
[2024-01-24 13:18:20,137] [INFO] Total running time: 0h1m9s