[2024-01-24 12:25:20,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference
[2024-01-24 12:25:21,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,847] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,847] [INFO] Running command: gunzip -c /var/lib/cwl/stgc59c1ba6-addb-4592-8ffb-45125e098e8d/GCF_014641075.1_ASM1464107v1_genomic.fna.gz | prodigal -d GCF_014641075.1_ASM1464107v1_genomic.fna/cds.fna -a GCF_014641075.1_ASM1464107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:44,212] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:44,213] [INFO] Task started: HMMsearch
[2024-01-24 12:25:44,213] [INFO] Running command: hmmsearch --tblout GCF_014641075.1_ASM1464107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference/reference_markers.hmm GCF_014641075.1_ASM1464107v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:44,584] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:44,585] [INFO] Found 6/6 markers.
[2024-01-24 12:25:44,648] [INFO] Query marker FASTA was written to GCF_014641075.1_ASM1464107v1_genomic.fna/markers.fasta
[2024-01-24 12:25:44,649] [INFO] Task started: Blastn
[2024-01-24 12:25:44,649] [INFO] Running command: blastn -query GCF_014641075.1_ASM1464107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference/reference_markers.fasta -out GCF_014641075.1_ASM1464107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:45,241] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:45,245] [INFO] Selected 24 target genomes.
[2024-01-24 12:25:45,245] [INFO] Target genome list was writen to GCF_014641075.1_ASM1464107v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:45,266] [INFO] Task started: fastANI
[2024-01-24 12:25:45,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59c1ba6-addb-4592-8ffb-45125e098e8d/GCF_014641075.1_ASM1464107v1_genomic.fna.gz --refList GCF_014641075.1_ASM1464107v1_genomic.fna/target_genomes.txt --output GCF_014641075.1_ASM1464107v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:26:11,633] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:11,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:26:11,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:26:11,658] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:26:11,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:26:11,659] [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 nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	100.0	2748	2749	95	conclusive
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	77.9234	308	2749	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.777	227	2749	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	77.686	127	2749	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.6362	287	2749	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.5508	267	2749	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.477	282	2749	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	77.4746	221	2749	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.4687	240	2749	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.4503	286	2749	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	77.326	122	2749	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	77.312	311	2749	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.3098	260	2749	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.2044	172	2749	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	76.9779	155	2749	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.9552	117	2749	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	76.8779	177	2749	95	below_threshold
Paenibacillus abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	76.8758	169	2749	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.7251	97	2749	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	76.6919	110	2749	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	76.6331	73	2749	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.5964	102	2749	95	below_threshold
Paenibacillus tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	76.222	99	2749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:26:11,661] [INFO] DFAST Taxonomy check result was written to GCF_014641075.1_ASM1464107v1_genomic.fna/tc_result.tsv
[2024-01-24 12:26:11,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:26:11,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:26:11,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference/checkm_data
[2024-01-24 12:26:11,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:26:11,742] [INFO] Task started: CheckM
[2024-01-24 12:26:11,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641075.1_ASM1464107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641075.1_ASM1464107v1_genomic.fna/checkm_input GCF_014641075.1_ASM1464107v1_genomic.fna/checkm_result
[2024-01-24 12:27:16,316] [INFO] Task succeeded: CheckM
[2024-01-24 12:27:16,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:27:16,349] [INFO] ===== Completeness check finished =====
[2024-01-24 12:27:16,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:27:16,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641075.1_ASM1464107v1_genomic.fna/markers.fasta)
[2024-01-24 12:27:16,350] [INFO] Task started: Blastn
[2024-01-24 12:27:16,350] [INFO] Running command: blastn -query GCF_014641075.1_ASM1464107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b88f5f6-98da-4709-ab56-139e9d655e28/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641075.1_ASM1464107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:17,137] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:17,142] [INFO] Selected 19 target genomes.
[2024-01-24 12:27:17,142] [INFO] Target genome list was writen to GCF_014641075.1_ASM1464107v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:27:17,238] [INFO] Task started: fastANI
[2024-01-24 12:27:17,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59c1ba6-addb-4592-8ffb-45125e098e8d/GCF_014641075.1_ASM1464107v1_genomic.fna.gz --refList GCF_014641075.1_ASM1464107v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641075.1_ASM1464107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:27:39,219] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:39,239] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:27:39,239] [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_014641075.1	s__Paenibacillus_Z nasutitermitis	100.0	2748	2749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017874275.1	s__Paenibacillus_Z sepulcri	81.0176	1011	2749	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_001280845.1	s__Paenibacillus_C sp001280845	78.1393	196	2749	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_001956295.1	s__Paenibacillus_C sp001956295	77.9874	163	2749	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_900106745.1	s__Paenibacillus_Z sp900106745	77.6022	268	2749	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_900116125.1	s__Paenibacillus_Z sp900116125	77.5502	264	2749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_001428245.1	s__Paenibacillus_C sp001428245	77.5227	190	2749	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_000422465.1	s__Paenibacillus_C harenae	77.4882	220	2749	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_010119935.1	s__Paenibacillus_Z lycopersici	77.4765	282	2749	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_009909185.1	s__Paenibacillus_Z glycinis	77.4503	286	2749	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_003386535.1	s__Paenibacillus_Z taihuensis	77.4436	240	2749	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_000961095.1	s__Paenibacillus_O beijingensis	77.2044	172	2749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513275.1	s__Paenibacillus_C gorillae	77.1454	163	2749	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_014705655.1	s__Paenibacillus_C sp014705655	77.0104	209	2749	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_003583765.1	s__Paenibacillus_C nanensis	76.9779	155	2749	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_014641555.1	s__Paenibacillus_C radicis	76.8854	179	2749	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_014640295.1	s__Paenibacillus_D abyssi	76.8758	169	2749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	76.6281	72	2749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705605.1	s__Paenibacillus_D sp014705605	76.411	121	2749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:27:39,243] [INFO] GTDB search result was written to GCF_014641075.1_ASM1464107v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:27:39,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:27:39,248] [INFO] DFAST_QC result json was written to GCF_014641075.1_ASM1464107v1_genomic.fna/dqc_result.json
[2024-01-24 12:27:39,248] [INFO] DFAST_QC completed!
[2024-01-24 12:27:39,248] [INFO] Total running time: 0h2m19s