[2024-01-24 13:49:40,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference
[2024-01-24 13:49:41,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,827] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,828] [INFO] Running command: gunzip -c /var/lib/cwl/stga4d9d2ef-f425-414c-968b-c93a521cf46d/GCF_003012835.1_ASM301283v1_genomic.fna.gz | prodigal -d GCF_003012835.1_ASM301283v1_genomic.fna/cds.fna -a GCF_003012835.1_ASM301283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:06,569] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:06,569] [INFO] Task started: HMMsearch
[2024-01-24 13:50:06,569] [INFO] Running command: hmmsearch --tblout GCF_003012835.1_ASM301283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference/reference_markers.hmm GCF_003012835.1_ASM301283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:07,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:07,022] [INFO] Found 6/6 markers.
[2024-01-24 13:50:07,086] [INFO] Query marker FASTA was written to GCF_003012835.1_ASM301283v1_genomic.fna/markers.fasta
[2024-01-24 13:50:07,086] [INFO] Task started: Blastn
[2024-01-24 13:50:07,087] [INFO] Running command: blastn -query GCF_003012835.1_ASM301283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference/reference_markers.fasta -out GCF_003012835.1_ASM301283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:07,703] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:07,708] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:07,709] [INFO] Target genome list was writen to GCF_003012835.1_ASM301283v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:07,717] [INFO] Task started: fastANI
[2024-01-24 13:50:07,718] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d9d2ef-f425-414c-968b-c93a521cf46d/GCF_003012835.1_ASM301283v1_genomic.fna.gz --refList GCF_003012835.1_ASM301283v1_genomic.fna/target_genomes.txt --output GCF_003012835.1_ASM301283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:28,613] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:28,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:28,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:28,622] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:50:28,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:28,622] [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=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	100.0	2159	2161	95	conclusive
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	99.9973	2160	2161	95	conclusive
Brevibacillus brevis	strain=DSM 30	GCA_003385915.1	1393	1393	suspected-type	True	99.9929	2151	2161	95	conclusive
Brevibacillus brevis	strain=NBRC 15304	GCA_006539845.1	1393	1393	suspected-type	True	99.9759	2085	2161	95	conclusive
Brevibacillus formosus	strain=NRRL NRS-863	GCA_003013405.1	54913	54913	type	True	93.8082	1821	2161	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	93.5529	1803	2161	95	below_threshold
Brevibacillus antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	92.6995	1685	2161	95	below_threshold
Brevibacillus fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	92.5947	1777	2161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,624] [INFO] DFAST Taxonomy check result was written to GCF_003012835.1_ASM301283v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:28,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:28,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:28,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference/checkm_data
[2024-01-24 13:50:28,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:28,692] [INFO] Task started: CheckM
[2024-01-24 13:50:28,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012835.1_ASM301283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012835.1_ASM301283v1_genomic.fna/checkm_input GCF_003012835.1_ASM301283v1_genomic.fna/checkm_result
[2024-01-24 13:51:38,780] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:38,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:38,808] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:38,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:38,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012835.1_ASM301283v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:38,809] [INFO] Task started: Blastn
[2024-01-24 13:51:38,809] [INFO] Running command: blastn -query GCF_003012835.1_ASM301283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33fb8de5-2329-41b6-a272-4a46a7db89f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012835.1_ASM301283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:39,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:39,549] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:39,549] [INFO] Target genome list was writen to GCF_003012835.1_ASM301283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:39,578] [INFO] Task started: fastANI
[2024-01-24 13:51:39,578] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d9d2ef-f425-414c-968b-c93a521cf46d/GCF_003012835.1_ASM301283v1_genomic.fna.gz --refList GCF_003012835.1_ASM301283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012835.1_ASM301283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:59,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:59,034] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:59,034] [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	99.9973	2160	2161	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	93.8082	1821	2161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_000282075.1	s__Brevibacillus sp000282075	93.7878	1819	2161	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	93.7861	1789	2161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_003013475.1	s__Brevibacillus porteri	93.5478	1803	2161	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	93.1327	1800	2161	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	92.757	1796	2161	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	92.7089	1684	2161	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	92.5783	1779	2161	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 13:51:59,036] [INFO] GTDB search result was written to GCF_003012835.1_ASM301283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:59,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:59,042] [INFO] DFAST_QC result json was written to GCF_003012835.1_ASM301283v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:59,042] [INFO] DFAST_QC completed!
[2024-01-24 13:51:59,042] [INFO] Total running time: 0h2m19s