[2024-01-24 13:30:11,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:11,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:11,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference
[2024-01-24 13:30:12,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:12,516] [INFO] Task started: Prodigal
[2024-01-24 13:30:12,517] [INFO] Running command: gunzip -c /var/lib/cwl/stg95cc09cf-cfae-45aa-b48f-d1887559796a/GCF_003268025.1_ASM326802v1_genomic.fna.gz | prodigal -d GCF_003268025.1_ASM326802v1_genomic.fna/cds.fna -a GCF_003268025.1_ASM326802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:30,137] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:30,138] [INFO] Task started: HMMsearch
[2024-01-24 13:30:30,138] [INFO] Running command: hmmsearch --tblout GCF_003268025.1_ASM326802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference/reference_markers.hmm GCF_003268025.1_ASM326802v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:30,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:30,478] [INFO] Found 6/6 markers.
[2024-01-24 13:30:30,530] [INFO] Query marker FASTA was written to GCF_003268025.1_ASM326802v1_genomic.fna/markers.fasta
[2024-01-24 13:30:30,530] [INFO] Task started: Blastn
[2024-01-24 13:30:30,531] [INFO] Running command: blastn -query GCF_003268025.1_ASM326802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference/reference_markers.fasta -out GCF_003268025.1_ASM326802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:31,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:31,171] [INFO] Selected 13 target genomes.
[2024-01-24 13:30:31,172] [INFO] Target genome list was writen to GCF_003268025.1_ASM326802v1_genomic.fna/target_genomes.txt
[2024-01-24 13:30:31,176] [INFO] Task started: fastANI
[2024-01-24 13:30:31,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg95cc09cf-cfae-45aa-b48f-d1887559796a/GCF_003268025.1_ASM326802v1_genomic.fna.gz --refList GCF_003268025.1_ASM326802v1_genomic.fna/target_genomes.txt --output GCF_003268025.1_ASM326802v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:48,194] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:48,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:48,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:48,205] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:30:48,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:48,206] [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 montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	100.0	2050	2050	95	conclusive
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	81.0251	1067	2050	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	79.874	818	2050	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	79.7737	744	2050	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	79.5687	752	2050	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	79.5542	722	2050	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	79.5468	685	2050	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	79.3043	695	2050	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	79.1651	692	2050	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	79.1436	689	2050	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.6263	307	2050	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.0348	201	2050	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.8242	231	2050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:48,208] [INFO] DFAST Taxonomy check result was written to GCF_003268025.1_ASM326802v1_genomic.fna/tc_result.tsv
[2024-01-24 13:30:48,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:48,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:48,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference/checkm_data
[2024-01-24 13:30:48,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:48,270] [INFO] Task started: CheckM
[2024-01-24 13:30:48,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003268025.1_ASM326802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003268025.1_ASM326802v1_genomic.fna/checkm_input GCF_003268025.1_ASM326802v1_genomic.fna/checkm_result
[2024-01-24 13:31:38,571] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:38,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:38,599] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:38,599] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:38,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003268025.1_ASM326802v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:38,600] [INFO] Task started: Blastn
[2024-01-24 13:31:38,600] [INFO] Running command: blastn -query GCF_003268025.1_ASM326802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b572b01-6a09-4a53-aabe-ef20edda0c15/dqc_reference/reference_markers_gtdb.fasta -out GCF_003268025.1_ASM326802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:39,405] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:39,410] [INFO] Selected 11 target genomes.
[2024-01-24 13:31:39,410] [INFO] Target genome list was writen to GCF_003268025.1_ASM326802v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:39,414] [INFO] Task started: fastANI
[2024-01-24 13:31:39,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg95cc09cf-cfae-45aa-b48f-d1887559796a/GCF_003268025.1_ASM326802v1_genomic.fna.gz --refList GCF_003268025.1_ASM326802v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003268025.1_ASM326802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:53,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:53,826] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:53,827] [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_003268025.1	s__Paenibacillus_Z montanisoli	100.0	2050	2050	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_900116125.1	s__Paenibacillus_Z sp900116125	81.0092	1055	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_900106745.1	s__Paenibacillus_Z sp900106745	80.8423	1007	2050	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_003386535.1	s__Paenibacillus_Z taihuensis	79.8871	816	2050	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_004342525.1	s__Paenibacillus_Z sp004342525	79.8662	777	2050	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	79.7699	744	2050	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_003952225.1	s__Paenibacillus_Z albus	79.5659	752	2050	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_009909185.1	s__Paenibacillus_Z glycinis	79.555	683	2050	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	79.5506	723	2050	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	79.2234	723	2050	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_009909195.1	s__Paenibacillus_Z sacheonensis	79.1617	693	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:53,828] [INFO] GTDB search result was written to GCF_003268025.1_ASM326802v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:53,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:53,833] [INFO] DFAST_QC result json was written to GCF_003268025.1_ASM326802v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:53,833] [INFO] DFAST_QC completed!
[2024-01-24 13:31:53,833] [INFO] Total running time: 0h1m43s