[2024-01-24 12:13:23,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference
[2024-01-24 12:13:26,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,486] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg7469633d-113a-4df5-8365-8ea58f01844a/GCF_030814985.1_ASM3081498v1_genomic.fna.gz | prodigal -d GCF_030814985.1_ASM3081498v1_genomic.fna/cds.fna -a GCF_030814985.1_ASM3081498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:41,881] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:41,881] [INFO] Task started: HMMsearch
[2024-01-24 12:13:41,881] [INFO] Running command: hmmsearch --tblout GCF_030814985.1_ASM3081498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference/reference_markers.hmm GCF_030814985.1_ASM3081498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:42,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:42,288] [INFO] Found 6/6 markers.
[2024-01-24 12:13:42,345] [INFO] Query marker FASTA was written to GCF_030814985.1_ASM3081498v1_genomic.fna/markers.fasta
[2024-01-24 12:13:42,346] [INFO] Task started: Blastn
[2024-01-24 12:13:42,346] [INFO] Running command: blastn -query GCF_030814985.1_ASM3081498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference/reference_markers.fasta -out GCF_030814985.1_ASM3081498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:42,983] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:42,986] [INFO] Selected 11 target genomes.
[2024-01-24 12:13:42,987] [INFO] Target genome list was writen to GCF_030814985.1_ASM3081498v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:42,991] [INFO] Task started: fastANI
[2024-01-24 12:13:42,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg7469633d-113a-4df5-8365-8ea58f01844a/GCF_030814985.1_ASM3081498v1_genomic.fna.gz --refList GCF_030814985.1_ASM3081498v1_genomic.fna/target_genomes.txt --output GCF_030814985.1_ASM3081498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:57,418] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:57,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:57,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:57,429] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:13:57,429] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:13:57,430] [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 kribbensis	strain=AM49	GCA_002240415.1	172713	172713	type	True	91.2088	1366	1792	95	below_threshold
Paenibacillus peoriae	strain=KCTC 3763	GCA_000236805.2	59893	59893	suspected-type	True	90.937	1339	1792	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	87.5225	1261	1792	95	below_threshold
Paenibacillus maysiensis	strain=1-49	GCA_000520815.1	1155954	1155954	type	True	86.3665	1236	1792	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	86.0488	1336	1792	95	below_threshold
Paenibacillus polymyxa	strain=NCTC10343	GCA_900454525.1	1406	1406	type	True	86.0	1355	1792	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_000217775.1	1406	1406	type	True	85.9652	1346	1792	95	below_threshold
Paenibacillus ottowii	strain=MS2379	GCA_006874425.1	2315729	2315729	type	True	85.6482	1330	1792	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.7003	128	1792	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.9323	92	1792	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.4922	122	1792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:57,437] [INFO] DFAST Taxonomy check result was written to GCF_030814985.1_ASM3081498v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:57,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:57,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:57,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference/checkm_data
[2024-01-24 12:13:57,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:57,509] [INFO] Task started: CheckM
[2024-01-24 12:13:57,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814985.1_ASM3081498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814985.1_ASM3081498v1_genomic.fna/checkm_input GCF_030814985.1_ASM3081498v1_genomic.fna/checkm_result
[2024-01-24 12:14:47,059] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:47,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,080] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:47,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:47,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814985.1_ASM3081498v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:47,081] [INFO] Task started: Blastn
[2024-01-24 12:14:47,081] [INFO] Running command: blastn -query GCF_030814985.1_ASM3081498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44ccb443-4b7e-4788-88e5-68955f34f15c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814985.1_ASM3081498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:48,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:48,073] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:48,073] [INFO] Target genome list was writen to GCF_030814985.1_ASM3081498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:48,081] [INFO] Task started: fastANI
[2024-01-24 12:14:48,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg7469633d-113a-4df5-8365-8ea58f01844a/GCF_030814985.1_ASM3081498v1_genomic.fna.gz --refList GCF_030814985.1_ASM3081498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814985.1_ASM3081498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:02,667] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:02,677] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:02,677] [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_009363115.1	s__Paenibacillus brasilensis	99.9991	1787	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.95	97.95	0.90	0.90	2	conclusive
GCF_002240415.1	s__Paenibacillus kribbensis	91.2212	1365	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.18	95.13	0.90	0.86	4	-
GCF_000236805.1	s__Paenibacillus peoriae	90.9196	1341	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719045.1	s__Paenibacillus polymyxa_B	87.184	1389	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.14	95.58	0.87	0.84	27	-
GCF_001709075.1	s__Paenibacillus polymyxa_D	87.041	1326	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.80	97.93	0.93	0.90	8	-
GCF_000235585.1	s__Paenibacillus terrae_B	86.649	1368	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943545.1	s__Paenibacillus terrae_A	86.3186	1299	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000237325.1	s__Paenibacillus polymyxa_C	86.1307	1364	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.50	97.87	0.93	0.89	15	-
GCF_015710975.1	s__Paenibacillus polymyxa	86.0162	1340	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.54	98.07	0.94	0.89	44	-
GCF_006874425.1	s__Paenibacillus ottowii	85.6416	1330	1792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.10	96.87	0.92	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:02,680] [INFO] GTDB search result was written to GCF_030814985.1_ASM3081498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:02,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:02,687] [INFO] DFAST_QC result json was written to GCF_030814985.1_ASM3081498v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:02,687] [INFO] DFAST_QC completed!
[2024-01-24 12:15:02,687] [INFO] Total running time: 0h1m39s