[2024-01-24 11:44:05,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference
[2024-01-24 11:44:08,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,839] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c67badd-b97f-4ef9-8c04-cbade752d884/GCF_013204855.1_ASM1320485v1_genomic.fna.gz | prodigal -d GCF_013204855.1_ASM1320485v1_genomic.fna/cds.fna -a GCF_013204855.1_ASM1320485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:31,095] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:31,095] [INFO] Task started: HMMsearch
[2024-01-24 11:44:31,095] [INFO] Running command: hmmsearch --tblout GCF_013204855.1_ASM1320485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference/reference_markers.hmm GCF_013204855.1_ASM1320485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:31,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:31,463] [INFO] Found 6/6 markers.
[2024-01-24 11:44:31,534] [INFO] Query marker FASTA was written to GCF_013204855.1_ASM1320485v1_genomic.fna/markers.fasta
[2024-01-24 11:44:31,534] [INFO] Task started: Blastn
[2024-01-24 11:44:31,534] [INFO] Running command: blastn -query GCF_013204855.1_ASM1320485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference/reference_markers.fasta -out GCF_013204855.1_ASM1320485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:32,120] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:32,124] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:32,124] [INFO] Target genome list was writen to GCF_013204855.1_ASM1320485v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:32,130] [INFO] Task started: fastANI
[2024-01-24 11:44:32,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c67badd-b97f-4ef9-8c04-cbade752d884/GCF_013204855.1_ASM1320485v1_genomic.fna.gz --refList GCF_013204855.1_ASM1320485v1_genomic.fna/target_genomes.txt --output GCF_013204855.1_ASM1320485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:52,149] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:52,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:52,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:52,164] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:52,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:52,165] [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 ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	94.6954	2382	2857	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	84.6476	1579	2857	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	82.1524	1095	2857	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	81.9603	1175	2857	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	81.8534	1081	2857	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	81.8492	1183	2857	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	81.8069	1059	2857	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	81.7785	1095	2857	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	81.5076	1046	2857	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	80.9732	1033	2857	95	below_threshold
Paenibacillus chitinolyticus	strain=NBRC 15660	GCA_000739915.1	79263	79263	type	True	77.3045	150	2857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:52,167] [INFO] DFAST Taxonomy check result was written to GCF_013204855.1_ASM1320485v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:52,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:52,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:52,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference/checkm_data
[2024-01-24 11:44:52,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:52,250] [INFO] Task started: CheckM
[2024-01-24 11:44:52,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013204855.1_ASM1320485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013204855.1_ASM1320485v1_genomic.fna/checkm_input GCF_013204855.1_ASM1320485v1_genomic.fna/checkm_result
[2024-01-24 11:45:57,764] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:57,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:57,792] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:57,793] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:57,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013204855.1_ASM1320485v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:57,794] [INFO] Task started: Blastn
[2024-01-24 11:45:57,794] [INFO] Running command: blastn -query GCF_013204855.1_ASM1320485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5898b404-590b-4463-a501-928571c984bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_013204855.1_ASM1320485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:58,599] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:58,603] [INFO] Selected 13 target genomes.
[2024-01-24 11:45:58,603] [INFO] Target genome list was writen to GCF_013204855.1_ASM1320485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:58,612] [INFO] Task started: fastANI
[2024-01-24 11:45:58,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c67badd-b97f-4ef9-8c04-cbade752d884/GCF_013204855.1_ASM1320485v1_genomic.fna.gz --refList GCF_013204855.1_ASM1320485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013204855.1_ASM1320485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:18,076] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:18,092] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:18,092] [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_013204855.1	s__Paenibacillus_E alba	100.0	2853	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002027705.1	s__Paenibacillus_E ferrarius	94.6959	2383	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640555.1	s__Paenibacillus_E marchantiophytorum	84.6236	1583	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141725.1	s__Paenibacillus_E planticolens	82.1454	1096	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103825.1	s__Paenibacillus_E sp900103825	82.1155	907	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141715.1	s__Paenibacillus_E phytorum	81.9387	1179	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	95.60	95.60	0.80	0.80	2	-
GCF_001426375.1	s__Paenibacillus_E sp001426375	81.7477	1117	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.92	98.92	0.95	0.95	2	-
GCF_001429545.1	s__Paenibacillus_E sp001429545	81.6911	1017	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799595.1	s__Paenibacillus_E chondroitinus_A	81.5591	1055	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411255.1	s__Paenibacillus_F sp000411255	77.4907	139	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	99.59	98.79	0.98	0.94	4	-
GCF_000739915.1	s__Paenibacillus_F chitinolyticus	77.3045	150	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107975.1	s__Paenibacillus_F sp900107975	76.8066	118	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829455.1	s__VKM-B-2647 sp000829455	76.4647	119	2857	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:18,094] [INFO] GTDB search result was written to GCF_013204855.1_ASM1320485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:18,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:18,098] [INFO] DFAST_QC result json was written to GCF_013204855.1_ASM1320485v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:18,098] [INFO] DFAST_QC completed!
[2024-01-24 11:46:18,098] [INFO] Total running time: 0h2m13s