[2024-01-24 13:13:23,786] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference
[2024-01-24 13:13:25,173] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,174] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg50c22239-6a6b-416d-93f5-228ec313ff94/GCF_008124765.1_ASM812476v1_genomic.fna.gz | prodigal -d GCF_008124765.1_ASM812476v1_genomic.fna/cds.fna -a GCF_008124765.1_ASM812476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:50,986] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:50,986] [INFO] Task started: HMMsearch
[2024-01-24 13:13:50,986] [INFO] Running command: hmmsearch --tblout GCF_008124765.1_ASM812476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference/reference_markers.hmm GCF_008124765.1_ASM812476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:51,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:51,453] [INFO] Found 6/6 markers.
[2024-01-24 13:13:51,514] [INFO] Query marker FASTA was written to GCF_008124765.1_ASM812476v1_genomic.fna/markers.fasta
[2024-01-24 13:13:51,514] [INFO] Task started: Blastn
[2024-01-24 13:13:51,515] [INFO] Running command: blastn -query GCF_008124765.1_ASM812476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference/reference_markers.fasta -out GCF_008124765.1_ASM812476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:52,154] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:52,158] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:52,158] [INFO] Target genome list was writen to GCF_008124765.1_ASM812476v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:52,490] [INFO] Task started: fastANI
[2024-01-24 13:13:52,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg50c22239-6a6b-416d-93f5-228ec313ff94/GCF_008124765.1_ASM812476v1_genomic.fna.gz --refList GCF_008124765.1_ASM812476v1_genomic.fna/target_genomes.txt --output GCF_008124765.1_ASM812476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:11,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:11,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:11,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:11,538] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:11,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:11,539] [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
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	100.0	2734	2735	95	conclusive
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	79.8354	1015	2735	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	78.5998	537	2735	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	78.4527	565	2735	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	78.4102	634	2735	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	78.1566	473	2735	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.729	445	2735	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.5985	360	2735	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.2777	247	2735	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	77.1874	336	2735	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.0254	217	2735	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	76.9397	218	2735	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.5369	216	2735	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.2202	205	2735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:11,541] [INFO] DFAST Taxonomy check result was written to GCF_008124765.1_ASM812476v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:11,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:11,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:11,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference/checkm_data
[2024-01-24 13:14:11,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:11,622] [INFO] Task started: CheckM
[2024-01-24 13:14:11,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124765.1_ASM812476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124765.1_ASM812476v1_genomic.fna/checkm_input GCF_008124765.1_ASM812476v1_genomic.fna/checkm_result
[2024-01-24 13:15:21,532] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:21,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:21,555] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:21,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:21,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124765.1_ASM812476v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:21,556] [INFO] Task started: Blastn
[2024-01-24 13:15:21,557] [INFO] Running command: blastn -query GCF_008124765.1_ASM812476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fd03551-d43b-442c-8e8d-92cf01222331/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124765.1_ASM812476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:22,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:22,405] [INFO] Selected 17 target genomes.
[2024-01-24 13:15:22,406] [INFO] Target genome list was writen to GCF_008124765.1_ASM812476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:22,442] [INFO] Task started: fastANI
[2024-01-24 13:15:22,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg50c22239-6a6b-416d-93f5-228ec313ff94/GCF_008124765.1_ASM812476v1_genomic.fna.gz --refList GCF_008124765.1_ASM812476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124765.1_ASM812476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:41,551] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:41,565] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:41,565] [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_008124765.1	s__Paenibacillus_Z methanolicus	100.0	2734	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014192105.1	s__Paenibacillus_Z phyllosphaerae	79.8392	1012	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	78.6024	536	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	78.5239	633	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	78.4529	565	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	78.1846	470	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268025.1	s__Paenibacillus_Z montanisoli	77.8883	404	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012676905.1	s__Paenibacillus_O sp012676905	77.7094	447	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386535.1	s__Paenibacillus_Z taihuensis	77.5985	360	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591485.1	s__Paenibacillus_C sp003591485	77.5888	237	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000598065.1	s__Paenibacillus_I darwinianus	77.3107	244	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	99.89	99.87	0.94	0.94	3	-
GCF_907165215.1	s__Thermobacillus xylanilyticus	77.1876	336	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_003851045.1	s__Paenibacillus_D sp003851045	77.0897	339	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513275.1	s__Paenibacillus_C gorillae	77.0254	217	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641555.1	s__Paenibacillus_C radicis	76.9514	217	2735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:41,567] [INFO] GTDB search result was written to GCF_008124765.1_ASM812476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:41,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:41,572] [INFO] DFAST_QC result json was written to GCF_008124765.1_ASM812476v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:41,572] [INFO] DFAST_QC completed!
[2024-01-24 13:15:41,572] [INFO] Total running time: 0h2m18s