[2024-01-24 13:49:33,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference
[2024-01-24 13:49:35,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:35,237] [INFO] Task started: Prodigal
[2024-01-24 13:49:35,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg78da8d94-178d-44d9-bb5d-77aa0eb9cabb/GCF_017652985.1_ASM1765298v1_genomic.fna.gz | prodigal -d GCF_017652985.1_ASM1765298v1_genomic.fna/cds.fna -a GCF_017652985.1_ASM1765298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,856] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,856] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,856] [INFO] Running command: hmmsearch --tblout GCF_017652985.1_ASM1765298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference/reference_markers.hmm GCF_017652985.1_ASM1765298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:56,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:56,333] [INFO] Found 6/6 markers.
[2024-01-24 13:49:56,392] [INFO] Query marker FASTA was written to GCF_017652985.1_ASM1765298v1_genomic.fna/markers.fasta
[2024-01-24 13:49:56,393] [INFO] Task started: Blastn
[2024-01-24 13:49:56,393] [INFO] Running command: blastn -query GCF_017652985.1_ASM1765298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference/reference_markers.fasta -out GCF_017652985.1_ASM1765298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,051] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,054] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:57,055] [INFO] Target genome list was writen to GCF_017652985.1_ASM1765298v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:57,059] [INFO] Task started: fastANI
[2024-01-24 13:49:57,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg78da8d94-178d-44d9-bb5d-77aa0eb9cabb/GCF_017652985.1_ASM1765298v1_genomic.fna.gz --refList GCF_017652985.1_ASM1765298v1_genomic.fna/target_genomes.txt --output GCF_017652985.1_ASM1765298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:17,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:17,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:17,183] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:17,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:17,184] [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 artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	100.0	2398	2403	95	conclusive
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	83.5966	1516	2403	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	82.4836	1235	2403	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	81.8133	1263	2403	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	81.7515	1289	2403	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	81.0947	1193	2403	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	78.7477	678	2403	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	78.3246	554	2403	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	78.2901	529	2403	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.4598	316	2403	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	76.9958	232	2403	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9411	207	2403	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	76.8127	254	2403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,186] [INFO] DFAST Taxonomy check result was written to GCF_017652985.1_ASM1765298v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:17,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:17,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:17,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference/checkm_data
[2024-01-24 13:50:17,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:17,263] [INFO] Task started: CheckM
[2024-01-24 13:50:17,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017652985.1_ASM1765298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017652985.1_ASM1765298v1_genomic.fna/checkm_input GCF_017652985.1_ASM1765298v1_genomic.fna/checkm_result
[2024-01-24 13:51:11,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:11,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:11,843] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:11,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:11,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017652985.1_ASM1765298v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:11,844] [INFO] Task started: Blastn
[2024-01-24 13:51:11,844] [INFO] Running command: blastn -query GCF_017652985.1_ASM1765298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b85c618-5b5b-4561-a5e1-63460ba00f8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_017652985.1_ASM1765298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:12,821] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:12,828] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:12,828] [INFO] Target genome list was writen to GCF_017652985.1_ASM1765298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:12,849] [INFO] Task started: fastANI
[2024-01-24 13:51:12,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg78da8d94-178d-44d9-bb5d-77aa0eb9cabb/GCF_017652985.1_ASM1765298v1_genomic.fna.gz --refList GCF_017652985.1_ASM1765298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017652985.1_ASM1765298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:27,836] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:27,850] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:27,850] [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_900113915.1	s__Paenibacillus_Z sp900113915	96.3948	2056	2403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	conclusive
GCF_009909185.1	s__Paenibacillus_Z glycinis	83.5905	1517	2403	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	82.5008	1232	2403	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_009909195.1	s__Paenibacillus_Z sacheonensis	81.7624	1287	2403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	81.106	1191	2403	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	78.7541	677	2403	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_014705655.1	s__Paenibacillus_C sp014705655	78.3226	602	2403	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_012676905.1	s__Paenibacillus_O sp012676905	78.2968	527	2403	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_018998565.1	s__Paenibacillus_G sp018998565	77.1532	243	2403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	77.0102	246	2403	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_004000865.1	s__Paenibacillus_G elgii	76.9155	232	2403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:27,852] [INFO] GTDB search result was written to GCF_017652985.1_ASM1765298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:27,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:27,859] [INFO] DFAST_QC result json was written to GCF_017652985.1_ASM1765298v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:27,859] [INFO] DFAST_QC completed!
[2024-01-24 13:51:27,859] [INFO] Total running time: 0h1m54s