[2024-01-24 10:47:40,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,788] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg804d403b-a1d8-4aa0-adec-8175289dc416/GCF_014645515.1_ASM1464551v1_genomic.fna.gz | prodigal -d GCF_014645515.1_ASM1464551v1_genomic.fna/cds.fna -a GCF_014645515.1_ASM1464551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:55,801] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:55,801] [INFO] Task started: HMMsearch
[2024-01-24 10:47:55,801] [INFO] Running command: hmmsearch --tblout GCF_014645515.1_ASM1464551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference/reference_markers.hmm GCF_014645515.1_ASM1464551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:56,134] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:56,136] [INFO] Found 6/6 markers.
[2024-01-24 10:47:56,177] [INFO] Query marker FASTA was written to GCF_014645515.1_ASM1464551v1_genomic.fna/markers.fasta
[2024-01-24 10:47:56,178] [INFO] Task started: Blastn
[2024-01-24 10:47:56,178] [INFO] Running command: blastn -query GCF_014645515.1_ASM1464551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference/reference_markers.fasta -out GCF_014645515.1_ASM1464551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:56,765] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:56,768] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:56,769] [INFO] Target genome list was writen to GCF_014645515.1_ASM1464551v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:56,790] [INFO] Task started: fastANI
[2024-01-24 10:47:56,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg804d403b-a1d8-4aa0-adec-8175289dc416/GCF_014645515.1_ASM1464551v1_genomic.fna.gz --refList GCF_014645515.1_ASM1464551v1_genomic.fna/target_genomes.txt --output GCF_014645515.1_ASM1464551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:09,597] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:09,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:09,608] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:09,608] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:09,608] [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
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	100.0	1792	1793	95	conclusive
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	90.4874	1368	1793	95	below_threshold
Oceanobacillus jeddahense	strain=S5	GCA_000750635.1	1462527	1462527	type	True	82.042	983	1793	95	below_threshold
Oceanobacillus timonensis	strain=Marseille-P3532	GCA_900166635.1	1926285	1926285	type	True	81.0414	831	1793	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	77.7726	198	1793	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	77.5884	168	1793	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.5139	182	1793	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.4616	168	1793	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	77.0904	85	1793	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	77.0792	123	1793	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.1168	65	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,610] [INFO] DFAST Taxonomy check result was written to GCF_014645515.1_ASM1464551v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:09,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:09,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:09,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference/checkm_data
[2024-01-24 10:48:09,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:09,663] [INFO] Task started: CheckM
[2024-01-24 10:48:09,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645515.1_ASM1464551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645515.1_ASM1464551v1_genomic.fna/checkm_input GCF_014645515.1_ASM1464551v1_genomic.fna/checkm_result
[2024-01-24 10:48:46,741] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:46,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,764] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:46,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:46,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645515.1_ASM1464551v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:46,765] [INFO] Task started: Blastn
[2024-01-24 10:48:46,765] [INFO] Running command: blastn -query GCF_014645515.1_ASM1464551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg890cd99a-82db-4b8a-ae02-9ae6e4a7f9ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645515.1_ASM1464551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:47,511] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:47,514] [INFO] Selected 7 target genomes.
[2024-01-24 10:48:47,514] [INFO] Target genome list was writen to GCF_014645515.1_ASM1464551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:47,552] [INFO] Task started: fastANI
[2024-01-24 10:48:47,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg804d403b-a1d8-4aa0-adec-8175289dc416/GCF_014645515.1_ASM1464551v1_genomic.fna.gz --refList GCF_014645515.1_ASM1464551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645515.1_ASM1464551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:58,810] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:58,822] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:58,822] [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_014645515.1	s__Oceanobacillus neutriphilus	100.0	1792	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900162665.1	s__Oceanobacillus sojae_A	91.4333	1374	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991515.1	s__Oceanobacillus sojae	90.4874	1368	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.95	98.95	0.93	0.93	2	-
GCF_009389585.1	s__Oceanobacillus sp009389585	83.121	965	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821065.1	s__Oceanobacillus oncorhynchi	82.2016	943	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.79	98.49	0.90	0.88	3	-
GCF_000750635.1	s__Oceanobacillus jeddahense	82.0534	980	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018333215.1	s__Oceanobacillus sp018333215	81.123	758	1793	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:58,824] [INFO] GTDB search result was written to GCF_014645515.1_ASM1464551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:58,825] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:58,829] [INFO] DFAST_QC result json was written to GCF_014645515.1_ASM1464551v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:58,829] [INFO] DFAST_QC completed!
[2024-01-24 10:48:58,829] [INFO] Total running time: 0h1m18s