[2024-01-24 13:12:54,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:54,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:54,440] [INFO] DQC Reference Directory: /var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference
[2024-01-24 13:12:55,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:55,873] [INFO] Task started: Prodigal
[2024-01-24 13:12:55,873] [INFO] Running command: gunzip -c /var/lib/cwl/stgd05b9431-1e9a-40f9-921c-c6170cda9835/GCF_011090185.1_ASM1109018v1_genomic.fna.gz | prodigal -d GCF_011090185.1_ASM1109018v1_genomic.fna/cds.fna -a GCF_011090185.1_ASM1109018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:09,725] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:09,725] [INFO] Task started: HMMsearch
[2024-01-24 13:13:09,725] [INFO] Running command: hmmsearch --tblout GCF_011090185.1_ASM1109018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference/reference_markers.hmm GCF_011090185.1_ASM1109018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:10,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:10,056] [INFO] Found 6/6 markers.
[2024-01-24 13:13:10,102] [INFO] Query marker FASTA was written to GCF_011090185.1_ASM1109018v1_genomic.fna/markers.fasta
[2024-01-24 13:13:10,103] [INFO] Task started: Blastn
[2024-01-24 13:13:10,103] [INFO] Running command: blastn -query GCF_011090185.1_ASM1109018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference/reference_markers.fasta -out GCF_011090185.1_ASM1109018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:10,792] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:10,796] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:10,796] [INFO] Target genome list was writen to GCF_011090185.1_ASM1109018v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:10,850] [INFO] Task started: fastANI
[2024-01-24 13:13:10,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05b9431-1e9a-40f9-921c-c6170cda9835/GCF_011090185.1_ASM1109018v1_genomic.fna.gz --refList GCF_011090185.1_ASM1109018v1_genomic.fna/target_genomes.txt --output GCF_011090185.1_ASM1109018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:31,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:31,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:31,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:31,179] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:31,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:31,180] [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
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	100.0	1784	1785	95	conclusive
Saccharibacillus brassicae	strain=ATSA2	GCA_006542275.1	2583377	2583377	type	True	82.9672	1256	1785	95	below_threshold
Saccharibacillus deserti	strain=WLJ055	GCA_013618475.1	1634444	1634444	type	True	82.0947	1229	1785	95	below_threshold
Saccharibacillus deserti	strain=KCTC 33693	GCA_013185225.1	1634444	1634444	type	True	82.0884	1230	1785	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	81.9744	1231	1785	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_013185185.1	2060666	2060666	type	True	81.5959	1191	1785	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	81.5877	1193	1785	95	below_threshold
Saccharibacillus sacchari	strain=DSM 19268	GCA_000585395.1	456493	456493	type	True	81.2797	1139	1785	95	below_threshold
Saccharibacillus kuerlensis	strain=DSM 22868	GCA_000378145.1	459527	459527	type	True	80.9662	1015	1785	95	below_threshold
Saccharibacillus kuerlensis	strain=CGMCC 1.6964	GCA_014645255.1	459527	459527	type	True	80.9003	1025	1785	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.0967	282	1785	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.0366	262	1785	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9808	254	1785	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.9194	187	1785	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.5425	125	1785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:31,182] [INFO] DFAST Taxonomy check result was written to GCF_011090185.1_ASM1109018v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:31,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:31,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:31,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference/checkm_data
[2024-01-24 13:13:31,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:31,259] [INFO] Task started: CheckM
[2024-01-24 13:13:31,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011090185.1_ASM1109018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011090185.1_ASM1109018v1_genomic.fna/checkm_input GCF_011090185.1_ASM1109018v1_genomic.fna/checkm_result
[2024-01-24 13:14:13,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:13,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,219] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:13,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:13,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011090185.1_ASM1109018v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:13,221] [INFO] Task started: Blastn
[2024-01-24 13:14:13,221] [INFO] Running command: blastn -query GCF_011090185.1_ASM1109018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bf234c-8fb9-4270-97b3-28fc84808daf/dqc_reference/reference_markers_gtdb.fasta -out GCF_011090185.1_ASM1109018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:14,073] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:14,076] [INFO] Selected 9 target genomes.
[2024-01-24 13:14:14,077] [INFO] Target genome list was writen to GCF_011090185.1_ASM1109018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:14,084] [INFO] Task started: fastANI
[2024-01-24 13:14:14,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05b9431-1e9a-40f9-921c-c6170cda9835/GCF_011090185.1_ASM1109018v1_genomic.fna.gz --refList GCF_011090185.1_ASM1109018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011090185.1_ASM1109018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:25,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:25,308] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:25,308] [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_011090185.1	s__Saccharibacillus alkalitolerans	100.0	1784	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002205895.1	s__Saccharibacillus sp002205895	82.977	1277	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542275.1	s__Saccharibacillus brassicae	82.9707	1255	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	97.06	97.06	0.95	0.95	2	-
GCF_013618475.1	s__Saccharibacillus deserti	82.1007	1228	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013185195.1	s__Saccharibacillus qingshengii	81.9658	1232	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185185.1	s__Saccharibacillus endophyticus	81.6039	1190	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000585395.1	s__Saccharibacillus sacchari	81.2645	1142	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378145.1	s__Saccharibacillus kuerlensis	80.9621	1015	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002189105.1	s__Saccharibacillus sp002189105	80.4313	992	1785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:25,310] [INFO] GTDB search result was written to GCF_011090185.1_ASM1109018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:25,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:25,315] [INFO] DFAST_QC result json was written to GCF_011090185.1_ASM1109018v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:25,316] [INFO] DFAST_QC completed!
[2024-01-24 13:14:25,316] [INFO] Total running time: 0h1m31s