[2024-01-25 18:11:20,697] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:20,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:20,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference
[2024-01-25 18:11:21,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:21,853] [INFO] Task started: Prodigal
[2024-01-25 18:11:21,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgc933f0cd-5df2-4eb1-9188-1271f1233974/GCF_900166635.1_PRJEB19430_genomic.fna.gz | prodigal -d GCF_900166635.1_PRJEB19430_genomic.fna/cds.fna -a GCF_900166635.1_PRJEB19430_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:30,689] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:30,690] [INFO] Task started: HMMsearch
[2024-01-25 18:11:30,690] [INFO] Running command: hmmsearch --tblout GCF_900166635.1_PRJEB19430_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference/reference_markers.hmm GCF_900166635.1_PRJEB19430_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:30,918] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:30,919] [INFO] Found 6/6 markers.
[2024-01-25 18:11:30,954] [INFO] Query marker FASTA was written to GCF_900166635.1_PRJEB19430_genomic.fna/markers.fasta
[2024-01-25 18:11:30,954] [INFO] Task started: Blastn
[2024-01-25 18:11:30,954] [INFO] Running command: blastn -query GCF_900166635.1_PRJEB19430_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference/reference_markers.fasta -out GCF_900166635.1_PRJEB19430_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:31,505] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:31,507] [INFO] Selected 11 target genomes.
[2024-01-25 18:11:31,508] [INFO] Target genome list was writen to GCF_900166635.1_PRJEB19430_genomic.fna/target_genomes.txt
[2024-01-25 18:11:31,515] [INFO] Task started: fastANI
[2024-01-25 18:11:31,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgc933f0cd-5df2-4eb1-9188-1271f1233974/GCF_900166635.1_PRJEB19430_genomic.fna.gz --refList GCF_900166635.1_PRJEB19430_genomic.fna/target_genomes.txt --output GCF_900166635.1_PRJEB19430_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:41,313] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:41,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:41,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:41,321] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:41,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:41,321] [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 timonensis	strain=Marseille-P3532	GCA_900166635.1	1926285	1926285	type	True	100.0	1494	1494	95	conclusive
Oceanobacillus jeddahense	strain=S5	GCA_000750635.1	1462527	1462527	type	True	82.9658	953	1494	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	81.0107	849	1494	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	80.8728	845	1494	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	78.336	177	1494	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.1794	116	1494	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	77.948	191	1494	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.1653	93	1494	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	77.0187	86	1494	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	76.827	86	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:41,322] [INFO] DFAST Taxonomy check result was written to GCF_900166635.1_PRJEB19430_genomic.fna/tc_result.tsv
[2024-01-25 18:11:41,323] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:41,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:41,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference/checkm_data
[2024-01-25 18:11:41,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:41,371] [INFO] Task started: CheckM
[2024-01-25 18:11:41,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900166635.1_PRJEB19430_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900166635.1_PRJEB19430_genomic.fna/checkm_input GCF_900166635.1_PRJEB19430_genomic.fna/checkm_result
[2024-01-25 18:12:10,722] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:10,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:10,743] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:10,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:10,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900166635.1_PRJEB19430_genomic.fna/markers.fasta)
[2024-01-25 18:12:10,744] [INFO] Task started: Blastn
[2024-01-25 18:12:10,744] [INFO] Running command: blastn -query GCF_900166635.1_PRJEB19430_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6d55ad-36d9-4aab-adab-dab84cdbad91/dqc_reference/reference_markers_gtdb.fasta -out GCF_900166635.1_PRJEB19430_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:11,570] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:11,572] [INFO] Selected 8 target genomes.
[2024-01-25 18:12:11,572] [INFO] Target genome list was writen to GCF_900166635.1_PRJEB19430_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:11,583] [INFO] Task started: fastANI
[2024-01-25 18:12:11,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgc933f0cd-5df2-4eb1-9188-1271f1233974/GCF_900166635.1_PRJEB19430_genomic.fna.gz --refList GCF_900166635.1_PRJEB19430_genomic.fna/target_genomes_gtdb.txt --output GCF_900166635.1_PRJEB19430_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:21,495] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:21,502] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:21,502] [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_900166635.1	s__Oceanobacillus timonensis	100.0	1494	1494	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000750635.1	s__Oceanobacillus jeddahense	82.9583	955	1494	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_000821065.1	s__Oceanobacillus oncorhynchi	82.8203	949	1494	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_009389585.1	s__Oceanobacillus sp009389585	81.312	843	1494	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_900162665.1	s__Oceanobacillus sojae_A	81.0732	850	1494	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_014645515.1	s__Oceanobacillus neutriphilus	81.0103	846	1494	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_007991515.1	s__Oceanobacillus sojae	80.919	838	1494	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_018333215.1	s__Oceanobacillus sp018333215	79.7209	642	1494	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:21,503] [INFO] GTDB search result was written to GCF_900166635.1_PRJEB19430_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:21,504] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:21,507] [INFO] DFAST_QC result json was written to GCF_900166635.1_PRJEB19430_genomic.fna/dqc_result.json
[2024-01-25 18:12:21,507] [INFO] DFAST_QC completed!
[2024-01-25 18:12:21,507] [INFO] Total running time: 0h1m1s