[2024-01-24 13:46:10,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,754] [INFO] DQC Reference Directory: /var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference
[2024-01-24 13:46:12,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,007] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg146423eb-bdcb-4a97-9aab-ad20f26e536a/GCF_014534655.1_ASM1453465v1_genomic.fna.gz | prodigal -d GCF_014534655.1_ASM1453465v1_genomic.fna/cds.fna -a GCF_014534655.1_ASM1453465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:31,536] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:31,537] [INFO] Task started: HMMsearch
[2024-01-24 13:46:31,537] [INFO] Running command: hmmsearch --tblout GCF_014534655.1_ASM1453465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference/reference_markers.hmm GCF_014534655.1_ASM1453465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:31,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:31,975] [INFO] Found 6/6 markers.
[2024-01-24 13:46:32,042] [INFO] Query marker FASTA was written to GCF_014534655.1_ASM1453465v1_genomic.fna/markers.fasta
[2024-01-24 13:46:32,042] [INFO] Task started: Blastn
[2024-01-24 13:46:32,042] [INFO] Running command: blastn -query GCF_014534655.1_ASM1453465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference/reference_markers.fasta -out GCF_014534655.1_ASM1453465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:32,682] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:32,685] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:32,686] [INFO] Target genome list was writen to GCF_014534655.1_ASM1453465v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:32,698] [INFO] Task started: fastANI
[2024-01-24 13:46:32,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg146423eb-bdcb-4a97-9aab-ad20f26e536a/GCF_014534655.1_ASM1453465v1_genomic.fna.gz --refList GCF_014534655.1_ASM1453465v1_genomic.fna/target_genomes.txt --output GCF_014534655.1_ASM1453465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:57,641] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:57,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:57,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:57,655] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:57,655] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:57,655] [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 germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	80.0396	779	2381	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	79.9377	788	2381	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	79.8188	720	2381	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	79.781	732	2381	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	79.7798	738	2381	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	79.6058	632	2381	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	79.5722	627	2381	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	79.5493	681	2381	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	79.3968	608	2381	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	79.3297	650	2381	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	79.2635	629	2381	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	79.2333	627	2381	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	78.9746	495	2381	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.7717	198	2381	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.7686	122	2381	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.1535	120	2381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:57,657] [INFO] DFAST Taxonomy check result was written to GCF_014534655.1_ASM1453465v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:57,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:57,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:57,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference/checkm_data
[2024-01-24 13:46:57,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:57,728] [INFO] Task started: CheckM
[2024-01-24 13:46:57,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014534655.1_ASM1453465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014534655.1_ASM1453465v1_genomic.fna/checkm_input GCF_014534655.1_ASM1453465v1_genomic.fna/checkm_result
[2024-01-24 13:47:54,105] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:54,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:54,128] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:54,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:54,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014534655.1_ASM1453465v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:54,129] [INFO] Task started: Blastn
[2024-01-24 13:47:54,129] [INFO] Running command: blastn -query GCF_014534655.1_ASM1453465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc159d3c6-c895-4f3e-b7e3-989969f602cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014534655.1_ASM1453465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:54,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:54,972] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:54,972] [INFO] Target genome list was writen to GCF_014534655.1_ASM1453465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:55,003] [INFO] Task started: fastANI
[2024-01-24 13:47:55,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg146423eb-bdcb-4a97-9aab-ad20f26e536a/GCF_014534655.1_ASM1453465v1_genomic.fna.gz --refList GCF_014534655.1_ASM1453465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014534655.1_ASM1453465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:21,215] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:21,228] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:21,229] [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_014534655.1	s__Paenibacillus_E sp014534655	100.0	2378	2381	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_001429545.1	s__Paenibacillus_E sp001429545	80.6179	826	2381	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	80.2359	827	2381	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_010820665.1	s__Paenibacillus_E sp010820665	80.2051	706	2381	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	79.9907	681	2381	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	79.9621	784	2381	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_000422905.1	s__Paenibacillus_E alginolyticus	79.7673	741	2381	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.46	96.94	0.87	0.75	3	-
GCF_013204855.1	s__Paenibacillus_E alba	79.6486	626	2381	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	79.6063	631	2381	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_002027705.1	s__Paenibacillus_E ferrarius	79.5675	628	2381	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_017874035.1	s__Paenibacillus_E aceris	79.5489	681	2381	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014640555.1	s__Paenibacillus_E marchantiophytorum	79.3894	610	2381	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_004000765.1	s__Paenibacillus_E chondroitinus	79.2596	630	2381	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	96.01	96.01	0.90	0.90	3	-
GCF_009882985.1	s__Paenibacillus_E silvestris	79.241	626	2381	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	79.1855	610	2381	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_013141695.1	s__Paenibacillus_E plantarum	78.975	494	2381	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 13:48:21,230] [INFO] GTDB search result was written to GCF_014534655.1_ASM1453465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:21,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:21,235] [INFO] DFAST_QC result json was written to GCF_014534655.1_ASM1453465v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:21,235] [INFO] DFAST_QC completed!
[2024-01-24 13:48:21,235] [INFO] Total running time: 0h2m10s