[2024-01-25 19:33:20,999] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:21,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:21,001] [INFO] DQC Reference Directory: /var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference
[2024-01-25 19:33:22,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,157] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,157] [INFO] Running command: gunzip -c /var/lib/cwl/stgec24ce58-3c88-49a1-a668-931203c29ddb/GCF_003385915.1_ASM338591v1_genomic.fna.gz | prodigal -d GCF_003385915.1_ASM338591v1_genomic.fna/cds.fna -a GCF_003385915.1_ASM338591v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:39,241] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:39,242] [INFO] Task started: HMMsearch
[2024-01-25 19:33:39,242] [INFO] Running command: hmmsearch --tblout GCF_003385915.1_ASM338591v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference/reference_markers.hmm GCF_003385915.1_ASM338591v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:39,536] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:39,538] [INFO] Found 6/6 markers.
[2024-01-25 19:33:39,592] [INFO] Query marker FASTA was written to GCF_003385915.1_ASM338591v1_genomic.fna/markers.fasta
[2024-01-25 19:33:39,593] [INFO] Task started: Blastn
[2024-01-25 19:33:39,593] [INFO] Running command: blastn -query GCF_003385915.1_ASM338591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference/reference_markers.fasta -out GCF_003385915.1_ASM338591v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:40,138] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:40,141] [INFO] Selected 19 target genomes.
[2024-01-25 19:33:40,142] [INFO] Target genome list was writen to GCF_003385915.1_ASM338591v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:40,147] [INFO] Task started: fastANI
[2024-01-25 19:33:40,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgec24ce58-3c88-49a1-a668-931203c29ddb/GCF_003385915.1_ASM338591v1_genomic.fna.gz --refList GCF_003385915.1_ASM338591v1_genomic.fna/target_genomes.txt --output GCF_003385915.1_ASM338591v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:01,394] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:01,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:01,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:01,405] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:34:01,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:01,405] [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 brevis	strain=DSM 30	GCA_003385915.1	1393	1393	suspected-type	True	100.0	2171	2173	95	conclusive
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	99.9979	2173	2173	95	conclusive
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	99.9886	2144	2173	95	conclusive
Brevibacillus brevis	strain=NBRC 15304	GCA_006539845.1	1393	1393	suspected-type	True	99.9751	2085	2173	95	conclusive
Brevibacillus formosus	strain=NRRL NRS-863	GCA_003013405.1	54913	54913	type	True	93.8386	1823	2173	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	93.5744	1810	2173	95	below_threshold
Brevibacillus antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	92.7121	1704	2173	95	below_threshold
Brevibacillus fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	92.6139	1783	2173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:01,406] [INFO] DFAST Taxonomy check result was written to GCF_003385915.1_ASM338591v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:01,407] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:01,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:01,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference/checkm_data
[2024-01-25 19:34:01,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:01,467] [INFO] Task started: CheckM
[2024-01-25 19:34:01,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385915.1_ASM338591v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385915.1_ASM338591v1_genomic.fna/checkm_input GCF_003385915.1_ASM338591v1_genomic.fna/checkm_result
[2024-01-25 19:34:51,806] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:51,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:51,828] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:51,828] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:51,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385915.1_ASM338591v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:51,830] [INFO] Task started: Blastn
[2024-01-25 19:34:51,830] [INFO] Running command: blastn -query GCF_003385915.1_ASM338591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4d8cda0-34dc-4899-a9b2-72e073d79363/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385915.1_ASM338591v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:52,526] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:52,528] [INFO] Selected 15 target genomes.
[2024-01-25 19:34:52,529] [INFO] Target genome list was writen to GCF_003385915.1_ASM338591v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:52,535] [INFO] Task started: fastANI
[2024-01-25 19:34:52,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgec24ce58-3c88-49a1-a668-931203c29ddb/GCF_003385915.1_ASM338591v1_genomic.fna.gz --refList GCF_003385915.1_ASM338591v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385915.1_ASM338591v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:13,145] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:13,152] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:13,152] [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_900637055.1	s__Brevibacillus brevis	99.9979	2173	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	conclusive
GCF_003013405.1	s__Brevibacillus formosus	93.8386	1823	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_001039275.2	s__Brevibacillus brevis_C	93.8288	1806	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_000282075.1	s__Brevibacillus sp000282075	93.7544	1817	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_003013475.1	s__Brevibacillus porteri	93.5811	1810	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_013284355.1	s__Brevibacillus sp013284355	93.1351	1804	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010165.1	s__Brevibacillus brevis_D	92.7768	1807	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_005217615.1	s__Brevibacillus antibioticus	92.7121	1704	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013395.1	s__Brevibacillus fortis	92.6161	1782	2173	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:13,154] [INFO] GTDB search result was written to GCF_003385915.1_ASM338591v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:13,155] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:13,157] [INFO] DFAST_QC result json was written to GCF_003385915.1_ASM338591v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:13,158] [INFO] DFAST_QC completed!
[2024-01-25 19:35:13,158] [INFO] Total running time: 0h1m52s