[2024-01-24 12:44:09,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:09,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:09,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference
[2024-01-24 12:44:10,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:10,486] [INFO] Task started: Prodigal
[2024-01-24 12:44:10,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg18e64a6b-e816-4e57-9114-6fe2bc980332/GCF_006861775.1_ASM686177v1_genomic.fna.gz | prodigal -d GCF_006861775.1_ASM686177v1_genomic.fna/cds.fna -a GCF_006861775.1_ASM686177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:18,891] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:18,891] [INFO] Task started: HMMsearch
[2024-01-24 12:44:18,891] [INFO] Running command: hmmsearch --tblout GCF_006861775.1_ASM686177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference/reference_markers.hmm GCF_006861775.1_ASM686177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:19,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:19,269] [INFO] Found 6/6 markers.
[2024-01-24 12:44:19,323] [INFO] Query marker FASTA was written to GCF_006861775.1_ASM686177v1_genomic.fna/markers.fasta
[2024-01-24 12:44:19,324] [INFO] Task started: Blastn
[2024-01-24 12:44:19,324] [INFO] Running command: blastn -query GCF_006861775.1_ASM686177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference/reference_markers.fasta -out GCF_006861775.1_ASM686177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:19,933] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:19,936] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:19,937] [INFO] Target genome list was writen to GCF_006861775.1_ASM686177v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:19,953] [INFO] Task started: fastANI
[2024-01-24 12:44:19,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg18e64a6b-e816-4e57-9114-6fe2bc980332/GCF_006861775.1_ASM686177v1_genomic.fna.gz --refList GCF_006861775.1_ASM686177v1_genomic.fna/target_genomes.txt --output GCF_006861775.1_ASM686177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:29,896] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:29,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:29,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:29,905] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:29,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:29,906] [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
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	100.0	1354	1358	95	conclusive
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	85.7321	990	1358	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	85.6063	995	1358	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	80.7042	626	1358	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	80.0871	574	1358	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	79.5777	442	1358	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	79.3326	362	1358	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.5422	165	1358	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	77.4522	165	1358	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.8295	77	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:29,910] [INFO] DFAST Taxonomy check result was written to GCF_006861775.1_ASM686177v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:29,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:29,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:29,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference/checkm_data
[2024-01-24 12:44:29,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:29,956] [INFO] Task started: CheckM
[2024-01-24 12:44:29,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006861775.1_ASM686177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006861775.1_ASM686177v1_genomic.fna/checkm_input GCF_006861775.1_ASM686177v1_genomic.fna/checkm_result
[2024-01-24 12:45:01,350] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:01,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:01,372] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:01,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:01,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006861775.1_ASM686177v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:01,373] [INFO] Task started: Blastn
[2024-01-24 12:45:01,373] [INFO] Running command: blastn -query GCF_006861775.1_ASM686177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4360ee46-e46f-4d32-8068-311c071ee8ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_006861775.1_ASM686177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:02,210] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:02,215] [INFO] Selected 10 target genomes.
[2024-01-24 12:45:02,216] [INFO] Target genome list was writen to GCF_006861775.1_ASM686177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:02,227] [INFO] Task started: fastANI
[2024-01-24 12:45:02,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg18e64a6b-e816-4e57-9114-6fe2bc980332/GCF_006861775.1_ASM686177v1_genomic.fna.gz --refList GCF_006861775.1_ASM686177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006861775.1_ASM686177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:11,401] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:11,415] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:11,415] [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_006861775.1	s__Psychrobacillus soli	100.0	1354	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111345.1	s__Psychrobacillus sp900111345	86.7166	969	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861795.1	s__Psychrobacillus lasiicapitis	85.7663	987	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007676755.1	s__Psychrobacillus sp007676755	82.182	716	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861825.1	s__Psychrobacillus vulpis	80.7096	625	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973485.1	s__Psychrobacillus glaciei	80.1307	569	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018140925.1	s__Psychrobacillus sp018140925	80.0063	521	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103605.1	s__Psychrobacillus sp900103605	79.8587	479	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115805.1	s__Psychrobacillus psychrotolerans	79.5777	442	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813185.1	s__Viridibacillus sp002813185	77.6276	168	1358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:11,416] [INFO] GTDB search result was written to GCF_006861775.1_ASM686177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:11,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:11,420] [INFO] DFAST_QC result json was written to GCF_006861775.1_ASM686177v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:11,420] [INFO] DFAST_QC completed!
[2024-01-24 12:45:11,421] [INFO] Total running time: 0h1m2s