[2024-01-24 13:18:33,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,694] [INFO] DQC Reference Directory: /var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference
[2024-01-24 13:18:34,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,965] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg61daf8af-7ab7-446e-b332-4bb025463c53/GCF_013141765.1_ASM1314176v1_genomic.fna.gz | prodigal -d GCF_013141765.1_ASM1314176v1_genomic.fna/cds.fna -a GCF_013141765.1_ASM1314176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:54,773] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:54,774] [INFO] Task started: HMMsearch
[2024-01-24 13:18:54,774] [INFO] Running command: hmmsearch --tblout GCF_013141765.1_ASM1314176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference/reference_markers.hmm GCF_013141765.1_ASM1314176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:55,177] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:55,178] [INFO] Found 6/6 markers.
[2024-01-24 13:18:55,240] [INFO] Query marker FASTA was written to GCF_013141765.1_ASM1314176v1_genomic.fna/markers.fasta
[2024-01-24 13:18:55,241] [INFO] Task started: Blastn
[2024-01-24 13:18:55,241] [INFO] Running command: blastn -query GCF_013141765.1_ASM1314176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference/reference_markers.fasta -out GCF_013141765.1_ASM1314176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:55,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:55,851] [INFO] Selected 21 target genomes.
[2024-01-24 13:18:55,852] [INFO] Target genome list was writen to GCF_013141765.1_ASM1314176v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:55,861] [INFO] Task started: fastANI
[2024-01-24 13:18:55,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg61daf8af-7ab7-446e-b332-4bb025463c53/GCF_013141765.1_ASM1314176v1_genomic.fna.gz --refList GCF_013141765.1_ASM1314176v1_genomic.fna/target_genomes.txt --output GCF_013141765.1_ASM1314176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:23,209] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:23,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:23,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:23,223] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:23,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:23,223] [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 foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	100.0	2560	2562	95	conclusive
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	79.1922	669	2562	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	78.3313	445	2562	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	78.111	164	2562	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	78.0788	165	2562	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	77.8992	383	2562	95	below_threshold
Paenibacillus xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	77.8516	232	2562	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.8471	347	2562	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	77.5234	171	2562	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	77.5233	171	2562	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	77.2256	131	2562	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	77.2054	84	2562	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	76.9762	212	2562	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	76.1774	62	2562	95	below_threshold
Paenibacillus senegalensis	strain=type strain: JC66	GCA_000285515.1	1465766	1465766	type	True	75.9949	55	2562	95	below_threshold
Paenibacillus turpanensis	strain=YIM B00363	GCA_011421635.1	2689078	2689078	type	True	75.4397	57	2562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:23,225] [INFO] DFAST Taxonomy check result was written to GCF_013141765.1_ASM1314176v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:23,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:23,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:23,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference/checkm_data
[2024-01-24 13:19:23,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:23,300] [INFO] Task started: CheckM
[2024-01-24 13:19:23,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013141765.1_ASM1314176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013141765.1_ASM1314176v1_genomic.fna/checkm_input GCF_013141765.1_ASM1314176v1_genomic.fna/checkm_result
[2024-01-24 13:20:20,134] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:20,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:20,162] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:20,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:20,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013141765.1_ASM1314176v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:20,163] [INFO] Task started: Blastn
[2024-01-24 13:20:20,163] [INFO] Running command: blastn -query GCF_013141765.1_ASM1314176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3da706d-e834-40c2-8a9f-0c47e1026d3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013141765.1_ASM1314176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:20,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:20,933] [INFO] Selected 23 target genomes.
[2024-01-24 13:20:20,933] [INFO] Target genome list was writen to GCF_013141765.1_ASM1314176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:20,963] [INFO] Task started: fastANI
[2024-01-24 13:20:20,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg61daf8af-7ab7-446e-b332-4bb025463c53/GCF_013141765.1_ASM1314176v1_genomic.fna.gz --refList GCF_013141765.1_ASM1314176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013141765.1_ASM1314176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:48,050] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:48,071] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:48,071] [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_013141765.1	s__Paenibacillus_S foliorum	100.0	2560	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004354045.1	s__Paenibacillus_S piri	79.1953	667	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017805.1	s__Paenibacillus_E sp008017805	78.9205	184	2562	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_001956045.1	s__Paenibacillus_S sp001956045	78.8669	504	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114475.1	s__Paenibacillus_S sp900114475	78.6274	452	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686845.1	s__Paenibacillus_S sp000686845	78.5432	424	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204855.1	s__Paenibacillus_E alba	78.3389	177	2562	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	78.111	164	2562	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	78.0866	162	2562	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_002234615.1	s__Paenibacillus_S rigui	77.9081	382	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217535.1	s__Paenibacillus_C sp003217535	77.8488	106	2562	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_002220865.2	s__Paenibacillus_S xerothermodurans	77.8457	232	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002042965.1	s__Paenibacillus_S sp002042965	77.8406	348	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	97.63	97.63	0.93	0.93	2	-
GCF_014534655.1	s__Paenibacillus_E sp014534655	77.5413	170	2562	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_000422465.1	s__Paenibacillus_C harenae	77.1048	83	2562	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_013359905.1	s__Paenibacillus taichungensis	77.0493	62	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.85	95.16	0.90	0.85	6	-
GCF_004307995.1	s__Paenibacillus_AF thalictri	76.9746	213	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101595.1	s__Paenibacillus_G sp900101595	76.9229	133	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110075.1	s__Paenibacillus_Z sp900110075	76.7723	70	2562	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	76.1943	52	2562	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_000285515.1	s__Paenibacillus_L senegalensis	75.9949	55	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011421635.1	s__Paenibacillus_AK turpanensis	75.459	56	2562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AK	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:48,073] [INFO] GTDB search result was written to GCF_013141765.1_ASM1314176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:48,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:48,078] [INFO] DFAST_QC result json was written to GCF_013141765.1_ASM1314176v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:48,078] [INFO] DFAST_QC completed!
[2024-01-24 13:20:48,078] [INFO] Total running time: 0h2m14s