[2024-01-24 12:06:11,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference
[2024-01-24 12:06:13,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,247] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgbda6d0ff-9760-4eab-80d0-141e454f57d5/GCF_002027705.1_ASM202770v1_genomic.fna.gz | prodigal -d GCF_002027705.1_ASM202770v1_genomic.fna/cds.fna -a GCF_002027705.1_ASM202770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:36,975] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:36,976] [INFO] Task started: HMMsearch
[2024-01-24 12:06:36,976] [INFO] Running command: hmmsearch --tblout GCF_002027705.1_ASM202770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference/reference_markers.hmm GCF_002027705.1_ASM202770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:37,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:37,520] [INFO] Found 6/6 markers.
[2024-01-24 12:06:37,618] [INFO] Query marker FASTA was written to GCF_002027705.1_ASM202770v1_genomic.fna/markers.fasta
[2024-01-24 12:06:37,618] [INFO] Task started: Blastn
[2024-01-24 12:06:37,619] [INFO] Running command: blastn -query GCF_002027705.1_ASM202770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference/reference_markers.fasta -out GCF_002027705.1_ASM202770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,269] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:38,270] [INFO] Target genome list was writen to GCF_002027705.1_ASM202770v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:38,278] [INFO] Task started: fastANI
[2024-01-24 12:06:38,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda6d0ff-9760-4eab-80d0-141e454f57d5/GCF_002027705.1_ASM202770v1_genomic.fna.gz --refList GCF_002027705.1_ASM202770v1_genomic.fna/target_genomes.txt --output GCF_002027705.1_ASM202770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:02,644] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:02,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:02,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:02,656] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:02,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:02,657] [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	100.0	3024	3027	95	conclusive
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	84.804	1589	3027	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	82.0533	1183	3027	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	81.9726	1226	3027	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	81.8768	1094	3027	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	81.875	1134	3027	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	81.8568	1100	3027	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	81.8417	1076	3027	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	81.0233	1075	3027	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	80.9221	1026	3027	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	80.7028	922	3027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:02,659] [INFO] DFAST Taxonomy check result was written to GCF_002027705.1_ASM202770v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:02,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:02,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:02,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference/checkm_data
[2024-01-24 12:07:02,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:02,749] [INFO] Task started: CheckM
[2024-01-24 12:07:02,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002027705.1_ASM202770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002027705.1_ASM202770v1_genomic.fna/checkm_input GCF_002027705.1_ASM202770v1_genomic.fna/checkm_result
[2024-01-24 12:08:11,941] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:11,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:11,987] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:11,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:11,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002027705.1_ASM202770v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:11,989] [INFO] Task started: Blastn
[2024-01-24 12:08:11,989] [INFO] Running command: blastn -query GCF_002027705.1_ASM202770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e0f18cd-23ee-4edb-bb64-be7e2ecb992a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002027705.1_ASM202770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:12,755] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:12,759] [INFO] Selected 10 target genomes.
[2024-01-24 12:08:12,759] [INFO] Target genome list was writen to GCF_002027705.1_ASM202770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:12,767] [INFO] Task started: fastANI
[2024-01-24 12:08:12,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda6d0ff-9760-4eab-80d0-141e454f57d5/GCF_002027705.1_ASM202770v1_genomic.fna.gz --refList GCF_002027705.1_ASM202770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002027705.1_ASM202770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:32,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:32,522] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:32,522] [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_002027705.1	s__Paenibacillus_E ferrarius	100.0	3024	3027	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_013204855.1	s__Paenibacillus_E alba	94.6646	2372	3027	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	84.7973	1590	3027	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	82.0474	1183	3027	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_900103825.1	s__Paenibacillus_E sp900103825	82.0422	932	3027	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_001426375.1	s__Paenibacillus_E sp001426375	81.8157	1145	3027	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	81.7972	1014	3027	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	81.7294	1084	3027	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_008017805.1	s__Paenibacillus_E sp008017805	81.3259	933	3027	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_000620565.1	s__Paenibacillus_E sp000620565	80.5821	813	3027	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:32,524] [INFO] GTDB search result was written to GCF_002027705.1_ASM202770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:32,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:32,528] [INFO] DFAST_QC result json was written to GCF_002027705.1_ASM202770v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:32,528] [INFO] DFAST_QC completed!
[2024-01-24 12:08:32,528] [INFO] Total running time: 0h2m21s