[2024-01-24 13:57:45,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:45,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:45,313] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference
[2024-01-24 13:57:46,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,678] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgc005f268-b561-476b-aecc-99b25ef602ad/GCF_003013405.1_ASM301340v1_genomic.fna.gz | prodigal -d GCF_003013405.1_ASM301340v1_genomic.fna/cds.fna -a GCF_003013405.1_ASM301340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:05,889] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:05,890] [INFO] Task started: HMMsearch
[2024-01-24 13:58:05,890] [INFO] Running command: hmmsearch --tblout GCF_003013405.1_ASM301340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference/reference_markers.hmm GCF_003013405.1_ASM301340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:06,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:06,246] [INFO] Found 6/6 markers.
[2024-01-24 13:58:06,313] [INFO] Query marker FASTA was written to GCF_003013405.1_ASM301340v1_genomic.fna/markers.fasta
[2024-01-24 13:58:06,314] [INFO] Task started: Blastn
[2024-01-24 13:58:06,314] [INFO] Running command: blastn -query GCF_003013405.1_ASM301340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference/reference_markers.fasta -out GCF_003013405.1_ASM301340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:06,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:06,932] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:06,932] [INFO] Target genome list was writen to GCF_003013405.1_ASM301340v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:06,937] [INFO] Task started: fastANI
[2024-01-24 13:58:06,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgc005f268-b561-476b-aecc-99b25ef602ad/GCF_003013405.1_ASM301340v1_genomic.fna.gz --refList GCF_003013405.1_ASM301340v1_genomic.fna/target_genomes.txt --output GCF_003013405.1_ASM301340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:21,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:21,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:21,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:21,472] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:21,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:21,473] [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
Brevibacillus formosus	strain=NRRL NRS-863	GCA_003013405.1	54913	54913	type	True	100.0	2027	2030	95	conclusive
Brevibacillus formosus	strain=DSM 9885	GCA_001012775.1	54913	54913	type	True	99.9866	2020	2030	95	conclusive
Brevibacillus formosus	strain=NBRC 15716	GCA_006540185.1	54913	54913	type	True	99.9775	1995	2030	95	conclusive
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	93.9223	1808	2030	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	93.9048	1815	2030	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	93.1708	1736	2030	95	below_threshold
Brevibacillus antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	93.0452	1664	2030	95	below_threshold
Brevibacillus marinus	strain=SCSIO 07484	GCA_003963515.1	2496837	2496837	type	True	77.0341	82	2030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,474] [INFO] DFAST Taxonomy check result was written to GCF_003013405.1_ASM301340v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:21,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:21,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:21,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference/checkm_data
[2024-01-24 13:58:21,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:21,534] [INFO] Task started: CheckM
[2024-01-24 13:58:21,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003013405.1_ASM301340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003013405.1_ASM301340v1_genomic.fna/checkm_input GCF_003013405.1_ASM301340v1_genomic.fna/checkm_result
[2024-01-24 13:59:19,136] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:19,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:19,160] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:19,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:19,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003013405.1_ASM301340v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:19,161] [INFO] Task started: Blastn
[2024-01-24 13:59:19,161] [INFO] Running command: blastn -query GCF_003013405.1_ASM301340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf88db3a-4fba-4acd-b185-b74c27e50b32/dqc_reference/reference_markers_gtdb.fasta -out GCF_003013405.1_ASM301340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:19,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:19,919] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:19,920] [INFO] Target genome list was writen to GCF_003013405.1_ASM301340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:19,928] [INFO] Task started: fastANI
[2024-01-24 13:59:19,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgc005f268-b561-476b-aecc-99b25ef602ad/GCF_003013405.1_ASM301340v1_genomic.fna.gz --refList GCF_003013405.1_ASM301340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003013405.1_ASM301340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:33,338] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:33,346] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:33,346] [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_003013405.1	s__Brevibacillus formosus	100.0	2027	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	conclusive
GCF_013284355.1	s__Brevibacillus sp013284355	94.1173	1811	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637055.1	s__Brevibacillus brevis	93.9048	1815	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_000282075.1	s__Brevibacillus sp000282075	93.4937	1760	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_001039275.2	s__Brevibacillus brevis_C	93.4673	1799	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_000010165.1	s__Brevibacillus brevis_D	93.4015	1799	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_003013475.1	s__Brevibacillus porteri	93.1708	1736	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_005217615.1	s__Brevibacillus antibioticus	93.0391	1665	2030	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:33,348] [INFO] GTDB search result was written to GCF_003013405.1_ASM301340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:33,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:33,352] [INFO] DFAST_QC result json was written to GCF_003013405.1_ASM301340v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:33,352] [INFO] DFAST_QC completed!
[2024-01-24 13:59:33,352] [INFO] Total running time: 0h1m48s