[2024-01-24 14:30:47,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,102] [INFO] DQC Reference Directory: /var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference
[2024-01-24 14:30:48,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,398] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,399] [INFO] Running command: gunzip -c /var/lib/cwl/stga132e477-9d7c-46c3-8c67-1ea05e907023/GCF_910594985.1_JJ-447_genomic.fna.gz | prodigal -d GCF_910594985.1_JJ-447_genomic.fna/cds.fna -a GCF_910594985.1_JJ-447_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:11,794] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:11,794] [INFO] Task started: HMMsearch
[2024-01-24 14:31:11,794] [INFO] Running command: hmmsearch --tblout GCF_910594985.1_JJ-447_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference/reference_markers.hmm GCF_910594985.1_JJ-447_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:12,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:12,284] [INFO] Found 6/6 markers.
[2024-01-24 14:31:12,349] [INFO] Query marker FASTA was written to GCF_910594985.1_JJ-447_genomic.fna/markers.fasta
[2024-01-24 14:31:12,349] [INFO] Task started: Blastn
[2024-01-24 14:31:12,350] [INFO] Running command: blastn -query GCF_910594985.1_JJ-447_genomic.fna/markers.fasta -db /var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference/reference_markers.fasta -out GCF_910594985.1_JJ-447_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,004] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,014] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:13,014] [INFO] Target genome list was writen to GCF_910594985.1_JJ-447_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,024] [INFO] Task started: fastANI
[2024-01-24 14:31:13,025] [INFO] Running command: fastANI --query /var/lib/cwl/stga132e477-9d7c-46c3-8c67-1ea05e907023/GCF_910594985.1_JJ-447_genomic.fna.gz --refList GCF_910594985.1_JJ-447_genomic.fna/target_genomes.txt --output GCF_910594985.1_JJ-447_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:33,340] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:33,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:33,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:33,354] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:33,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:33,355] [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 allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	100.0	2662	2668	95	conclusive
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	78.7443	482	2668	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	78.7212	497	2668	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	78.6285	516	2668	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	78.5666	458	2668	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	78.351	425	2668	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	78.1284	371	2668	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.8322	512	2668	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	77.651	227	2668	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.6046	397	2668	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9895	158	2668	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	76.9595	96	2668	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.8397	127	2668	95	below_threshold
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	76.7451	105	2668	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	76.5122	129	2668	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.418	122	2668	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.3489	127	2668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,356] [INFO] DFAST Taxonomy check result was written to GCF_910594985.1_JJ-447_genomic.fna/tc_result.tsv
[2024-01-24 14:31:33,357] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:33,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:33,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference/checkm_data
[2024-01-24 14:31:33,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:33,438] [INFO] Task started: CheckM
[2024-01-24 14:31:33,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_910594985.1_JJ-447_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_910594985.1_JJ-447_genomic.fna/checkm_input GCF_910594985.1_JJ-447_genomic.fna/checkm_result
[2024-01-24 14:32:40,810] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:40,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:40,835] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:40,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:40,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_910594985.1_JJ-447_genomic.fna/markers.fasta)
[2024-01-24 14:32:40,837] [INFO] Task started: Blastn
[2024-01-24 14:32:40,837] [INFO] Running command: blastn -query GCF_910594985.1_JJ-447_genomic.fna/markers.fasta -db /var/lib/cwl/stgf93f278c-9e2d-4154-8175-ad7334e7158f/dqc_reference/reference_markers_gtdb.fasta -out GCF_910594985.1_JJ-447_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:41,635] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:41,640] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:41,640] [INFO] Target genome list was writen to GCF_910594985.1_JJ-447_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:41,651] [INFO] Task started: fastANI
[2024-01-24 14:32:41,651] [INFO] Running command: fastANI --query /var/lib/cwl/stga132e477-9d7c-46c3-8c67-1ea05e907023/GCF_910594985.1_JJ-447_genomic.fna.gz --refList GCF_910594985.1_JJ-447_genomic.fna/target_genomes_gtdb.txt --output GCF_910594985.1_JJ-447_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:00,439] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:00,455] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:00,455] [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_910594985.1	s__Paenibacillus_G sp910594985	100.0	2662	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_910593845.1	s__Paenibacillus_G solanacearum	84.837	1795	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786445.1	s__Paenibacillus_G sp007786445	78.8971	585	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	78.7621	479	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	78.7318	485	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000865.1	s__Paenibacillus_G elgii	78.7255	496	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	78.6243	516	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_900100345.1	s__Paenibacillus_G tianmuensis	78.5672	456	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833255.1	s__Paenibacillus_G sp017833255	78.2272	289	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000250655.1	s__Paenibacillus_G mucilaginosus	78.1999	375	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.86	98.79	0.96	0.95	3	-
GCF_004000985.1	s__Paenibacillus_G validus	78.1378	370	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	-
GCF_008017805.1	s__Paenibacillus_E sp008017805	77.6143	109	2668	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_001685395.1	s__Paenibacillus_A yonginensis	76.97	94	2668	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_001653565.1	s__Paenibacillus_E oryzisoli	76.7451	105	2668	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_004345425.1	s__Paenibacillus_C sp004345425	76.5794	141	2668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:00,457] [INFO] GTDB search result was written to GCF_910594985.1_JJ-447_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:00,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:00,462] [INFO] DFAST_QC result json was written to GCF_910594985.1_JJ-447_genomic.fna/dqc_result.json
[2024-01-24 14:33:00,462] [INFO] DFAST_QC completed!
[2024-01-24 14:33:00,463] [INFO] Total running time: 0h2m13s