[2024-01-24 14:22:01,169] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,172] [INFO] DQC Reference Directory: /var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference
[2024-01-24 14:22:02,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,384] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg77410c64-5958-4417-9ce6-e26dcd68af30/GCF_016908255.1_ASM1690825v1_genomic.fna.gz | prodigal -d GCF_016908255.1_ASM1690825v1_genomic.fna/cds.fna -a GCF_016908255.1_ASM1690825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:23,313] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:23,313] [INFO] Task started: HMMsearch
[2024-01-24 14:22:23,313] [INFO] Running command: hmmsearch --tblout GCF_016908255.1_ASM1690825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference/reference_markers.hmm GCF_016908255.1_ASM1690825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:23,615] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:23,616] [INFO] Found 6/6 markers.
[2024-01-24 14:22:23,670] [INFO] Query marker FASTA was written to GCF_016908255.1_ASM1690825v1_genomic.fna/markers.fasta
[2024-01-24 14:22:23,670] [INFO] Task started: Blastn
[2024-01-24 14:22:23,670] [INFO] Running command: blastn -query GCF_016908255.1_ASM1690825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference/reference_markers.fasta -out GCF_016908255.1_ASM1690825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:24,274] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:24,277] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:24,277] [INFO] Target genome list was writen to GCF_016908255.1_ASM1690825v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:24,282] [INFO] Task started: fastANI
[2024-01-24 14:22:24,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg77410c64-5958-4417-9ce6-e26dcd68af30/GCF_016908255.1_ASM1690825v1_genomic.fna.gz --refList GCF_016908255.1_ASM1690825v1_genomic.fna/target_genomes.txt --output GCF_016908255.1_ASM1690825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:39,308] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:39,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:39,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:39,328] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:39,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:39,328] [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 sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	100.0	2454	2459	95	conclusive
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	99.9967	2445	2459	95	conclusive
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	82.6552	1375	2459	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	82.5309	1297	2459	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	82.2431	1255	2459	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	81.6984	1295	2459	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	78.8251	692	2459	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.455	365	2459	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.1811	352	2459	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.1682	206	2459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:39,330] [INFO] DFAST Taxonomy check result was written to GCF_016908255.1_ASM1690825v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:39,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:39,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:39,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference/checkm_data
[2024-01-24 14:22:39,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:39,407] [INFO] Task started: CheckM
[2024-01-24 14:22:39,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908255.1_ASM1690825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908255.1_ASM1690825v1_genomic.fna/checkm_input GCF_016908255.1_ASM1690825v1_genomic.fna/checkm_result
[2024-01-24 14:23:37,089] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:37,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:37,113] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:37,113] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:37,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908255.1_ASM1690825v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:37,113] [INFO] Task started: Blastn
[2024-01-24 14:23:37,114] [INFO] Running command: blastn -query GCF_016908255.1_ASM1690825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge98e239f-4cc6-42a9-8769-b140159d2089/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908255.1_ASM1690825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:37,883] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:37,886] [INFO] Selected 6 target genomes.
[2024-01-24 14:23:37,886] [INFO] Target genome list was writen to GCF_016908255.1_ASM1690825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:37,890] [INFO] Task started: fastANI
[2024-01-24 14:23:37,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg77410c64-5958-4417-9ce6-e26dcd68af30/GCF_016908255.1_ASM1690825v1_genomic.fna.gz --refList GCF_016908255.1_ASM1690825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908255.1_ASM1690825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:48,612] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:48,620] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:48,621] [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_009909195.1	s__Paenibacillus_Z sacheonensis	99.9967	2445	2459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009909185.1	s__Paenibacillus_Z glycinis	82.6676	1373	2459	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	82.5389	1296	2459	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	82.2316	1257	2459	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	81.7244	1296	2459	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_900106745.1	s__Paenibacillus_Z sp900106745	78.8345	610	2459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:48,622] [INFO] GTDB search result was written to GCF_016908255.1_ASM1690825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:48,622] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:48,625] [INFO] DFAST_QC result json was written to GCF_016908255.1_ASM1690825v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:48,625] [INFO] DFAST_QC completed!
[2024-01-24 14:23:48,625] [INFO] Total running time: 0h1m47s