[2024-01-25 17:51:50,697] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference
[2024-01-25 17:51:51,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:51,861] [INFO] Task started: Prodigal
[2024-01-25 17:51:51,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg034e75bb-ec95-4fe4-a7dd-47193e936d2e/GCF_000430765.1_ASM43076v1_genomic.fna.gz | prodigal -d GCF_000430765.1_ASM43076v1_genomic.fna/cds.fna -a GCF_000430765.1_ASM43076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:02,239] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:02,239] [INFO] Task started: HMMsearch
[2024-01-25 17:52:02,239] [INFO] Running command: hmmsearch --tblout GCF_000430765.1_ASM43076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference/reference_markers.hmm GCF_000430765.1_ASM43076v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:02,537] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:02,538] [INFO] Found 6/6 markers.
[2024-01-25 17:52:02,580] [INFO] Query marker FASTA was written to GCF_000430765.1_ASM43076v1_genomic.fna/markers.fasta
[2024-01-25 17:52:02,580] [INFO] Task started: Blastn
[2024-01-25 17:52:02,580] [INFO] Running command: blastn -query GCF_000430765.1_ASM43076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference/reference_markers.fasta -out GCF_000430765.1_ASM43076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:03,130] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:03,135] [INFO] Selected 22 target genomes.
[2024-01-25 17:52:03,136] [INFO] Target genome list was writen to GCF_000430765.1_ASM43076v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:03,153] [INFO] Task started: fastANI
[2024-01-25 17:52:03,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg034e75bb-ec95-4fe4-a7dd-47193e936d2e/GCF_000430765.1_ASM43076v1_genomic.fna.gz --refList GCF_000430765.1_ASM43076v1_genomic.fna/target_genomes.txt --output GCF_000430765.1_ASM43076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:19,038] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:19,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:19,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:19,047] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:19,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:19,048] [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
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	100.0	1660	1665	95	conclusive
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	78.3771	326	1665	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	78.1666	85	1665	95	below_threshold
Peribacillus glennii	strain=V44-8	GCA_003429105.1	2303991	2303991	type	True	77.8803	132	1665	95	below_threshold
Peribacillus saganii	strain=V47-23a	GCA_003429095.1	2303992	2303992	type	True	77.7946	108	1665	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.7382	95	1665	95	below_threshold
Bacillus salacetis	strain=SKP7-4	GCA_003581585.1	2315464	2315464	type	True	77.4789	69	1665	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.3965	108	1665	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	77.19	65	1665	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	76.9208	76	1665	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.9206	80	1665	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.851	96	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:19,049] [INFO] DFAST Taxonomy check result was written to GCF_000430765.1_ASM43076v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:19,050] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:19,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:19,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference/checkm_data
[2024-01-25 17:52:19,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:19,102] [INFO] Task started: CheckM
[2024-01-25 17:52:19,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430765.1_ASM43076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430765.1_ASM43076v1_genomic.fna/checkm_input GCF_000430765.1_ASM43076v1_genomic.fna/checkm_result
[2024-01-25 17:52:52,924] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:52,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:52,946] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:52,946] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:52,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430765.1_ASM43076v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:52,947] [INFO] Task started: Blastn
[2024-01-25 17:52:52,947] [INFO] Running command: blastn -query GCF_000430765.1_ASM43076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c9dc02-7bcb-4a94-b001-744e08ee5e7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430765.1_ASM43076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:53,763] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:53,766] [INFO] Selected 27 target genomes.
[2024-01-25 17:52:53,766] [INFO] Target genome list was writen to GCF_000430765.1_ASM43076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:53,792] [INFO] Task started: fastANI
[2024-01-25 17:52:53,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg034e75bb-ec95-4fe4-a7dd-47193e936d2e/GCF_000430765.1_ASM43076v1_genomic.fna.gz --refList GCF_000430765.1_ASM43076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430765.1_ASM43076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:15,337] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:15,352] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:15,353] [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_000430765.1	s__Bacillus_AI kribbensis	100.0	1660	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002863585.1	s__Bacillus_AI deserti_A	79.091	353	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909175.1	s__Bacillus_AI deserti	78.4009	324	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860285.1	s__Peribacillus_A sp002860285	78.3961	121	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112495.1	s__Peribacillus sp900112495	78.3505	148	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	95.26	95.26	0.85	0.85	2	-
GCF_001578185.1	s__Peribacillus simplex_A	78.1532	87	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.63	97.17	0.91	0.91	3	-
GCF_003429105.1	s__Peribacillus glennii	77.9325	130	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	77.7902	95	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303275.1	s__Cytobacillus sp017303275	77.4739	103	1665	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_003429085.1	s__Peribacillus sp003429085	77.323	111	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685025.1	s__Bacillus_D sp001685025	77.3163	74	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860165.1	s__Bacillus_BJ sp002860165	77.2923	79	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956215.1	s__Cytobacillus sp001956215	77.2805	101	1665	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_001038755.1	s__Cytobacillus firmus_B	77.2411	103	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	97.85	96.97	0.92	0.91	5	-
GCF_001183965.1	s__Pradoshia sp001183965	77.1965	75	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710145.1	s__Bacillus_BD endozanthoxylicus	77.0686	77	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180415.1	s__Bacillus_BM vietnamensis_B	77.0579	75	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989135.1	s__Peribacillus cavernae	77.0498	115	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668575.1	s__Falsibacillus albus	77.0129	77	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272225.1	s__Cytobacillus sp002272225	76.9645	90	1665	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_001591465.1	s__Cytobacillus firmus	76.8567	93	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.21	98.02	0.95	0.85	11	-
GCF_008180615.1	s__Bacillus_BM vietnamensis_A	76.8553	90	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	98.11	98.11	0.91	0.91	2	-
GCF_004138295.1	s__Ectobacillus funiculus	76.6663	65	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Ectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181495.1	s__Bacillus_BM sp000181495	76.5595	52	1665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:15,354] [INFO] GTDB search result was written to GCF_000430765.1_ASM43076v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:15,355] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:15,360] [INFO] DFAST_QC result json was written to GCF_000430765.1_ASM43076v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:15,360] [INFO] DFAST_QC completed!
[2024-01-25 17:53:15,360] [INFO] Total running time: 0h1m25s