[2024-01-25 20:21:50,418] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:50,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:50,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference
[2024-01-25 20:21:51,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:51,562] [INFO] Task started: Prodigal
[2024-01-25 20:21:51,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg0da65d26-c5a4-4afb-86a6-f997614c963e/GCF_003233845.1_ASM323384v1_genomic.fna.gz | prodigal -d GCF_003233845.1_ASM323384v1_genomic.fna/cds.fna -a GCF_003233845.1_ASM323384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:05,983] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:05,984] [INFO] Task started: HMMsearch
[2024-01-25 20:22:05,984] [INFO] Running command: hmmsearch --tblout GCF_003233845.1_ASM323384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference/reference_markers.hmm GCF_003233845.1_ASM323384v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:06,427] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:06,429] [INFO] Found 6/6 markers.
[2024-01-25 20:22:06,473] [INFO] Query marker FASTA was written to GCF_003233845.1_ASM323384v1_genomic.fna/markers.fasta
[2024-01-25 20:22:06,474] [INFO] Task started: Blastn
[2024-01-25 20:22:06,474] [INFO] Running command: blastn -query GCF_003233845.1_ASM323384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference/reference_markers.fasta -out GCF_003233845.1_ASM323384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:07,031] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:07,034] [INFO] Selected 23 target genomes.
[2024-01-25 20:22:07,034] [INFO] Target genome list was writen to GCF_003233845.1_ASM323384v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:07,053] [INFO] Task started: fastANI
[2024-01-25 20:22:07,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da65d26-c5a4-4afb-86a6-f997614c963e/GCF_003233845.1_ASM323384v1_genomic.fna.gz --refList GCF_003233845.1_ASM323384v1_genomic.fna/target_genomes.txt --output GCF_003233845.1_ASM323384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:32,795] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:32,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:32,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:32,809] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:32,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:32,809] [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 sambharensis	strain=SMB1	GCA_003233845.1	1803190	1803190	type	True	100.0	1863	1865	95	conclusive
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	87.3153	1405	1865	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	78.0089	201	1865	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.3047	170	1865	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	77.2896	163	1865	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.181	113	1865	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	77.1517	176	1865	95	below_threshold
Paenibacillus curdlanolyticus	strain=YK9	GCA_000179615.1	59840	59840	type	True	77.1181	145	1865	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.1049	145	1865	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	77.0768	197	1865	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.0626	147	1865	95	below_threshold
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	77.0545	165	1865	95	below_threshold
Paenibacillus cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	77.0229	136	1865	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.9739	212	1865	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	76.8055	136	1865	95	below_threshold
Paenibacillus xylaniclasticus	strain=NBRC 106381	GCA_004001065.1	588083	588083	type	True	76.7963	129	1865	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.7651	183	1865	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	76.7263	152	1865	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	76.7029	168	1865	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.5056	132	1865	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.4319	155	1865	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.3832	139	1865	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.1973	98	1865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:32,810] [INFO] DFAST Taxonomy check result was written to GCF_003233845.1_ASM323384v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:32,811] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:32,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:32,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference/checkm_data
[2024-01-25 20:22:32,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:32,862] [INFO] Task started: CheckM
[2024-01-25 20:22:32,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003233845.1_ASM323384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003233845.1_ASM323384v1_genomic.fna/checkm_input GCF_003233845.1_ASM323384v1_genomic.fna/checkm_result
[2024-01-25 20:23:16,553] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:16,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:16,575] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:16,575] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:16,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003233845.1_ASM323384v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:16,576] [INFO] Task started: Blastn
[2024-01-25 20:23:16,576] [INFO] Running command: blastn -query GCF_003233845.1_ASM323384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30e36092-c1ab-46c5-aed3-5932c99a2331/dqc_reference/reference_markers_gtdb.fasta -out GCF_003233845.1_ASM323384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:17,363] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:17,366] [INFO] Selected 27 target genomes.
[2024-01-25 20:23:17,367] [INFO] Target genome list was writen to GCF_003233845.1_ASM323384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:17,388] [INFO] Task started: fastANI
[2024-01-25 20:23:17,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da65d26-c5a4-4afb-86a6-f997614c963e/GCF_003233845.1_ASM323384v1_genomic.fna.gz --refList GCF_003233845.1_ASM323384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003233845.1_ASM323384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:47,889] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:47,904] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:47,904] [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_003233845.1	s__Paenibacillus_I sambharensis	100.0	1863	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000598065.1	s__Paenibacillus_I darwinianus	78.0034	202	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	99.89	99.87	0.94	0.94	3	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	77.2882	169	1865	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_000422505.1	s__Paenibacillus_D pinihumi	77.2875	164	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	99.89	99.89	1.00	1.00	2	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	77.2088	146	1865	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	77.1505	177	1865	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_004342525.1	s__Paenibacillus_Z sp004342525	77.1492	155	1865	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_003952225.1	s__Paenibacillus_Z albus	77.1489	149	1865	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_000179615.1	s__Paenibacillus_T curdlanolyticus	77.1181	145	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386535.1	s__Paenibacillus_Z taihuensis	77.1049	145	1865	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_000250655.1	s__Paenibacillus_G mucilaginosus	77.0576	164	1865	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_003605435.1	s__Paenibacillus_C pinisoli	77.0492	178	1865	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_900110075.1	s__Paenibacillus_Z sp900110075	77.0278	137	1865	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_003851045.1	s__Paenibacillus_D sp003851045	77.0136	204	1865	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_000023585.1	s__Paenibacillus_C sp000023585	76.9997	154	1865	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_003182255.1	s__Paenibacillus_T cellulosilyticus	76.9892	135	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008124765.1	s__Paenibacillus_Z methanolicus	76.9669	211	1865	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	76.897	175	1865	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_001280845.1	s__Paenibacillus_C sp001280845	76.8701	90	1865	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_011947265.1	s__Paenibacillus_C sp011947265	76.8559	150	1865	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_910593845.1	s__Paenibacillus_G solanacearum	76.818	101	1865	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_003112455.1	s__Paenibacillus_C agaridevorans	76.748	139	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCF_014641555.1	s__Paenibacillus_C radicis	76.7263	152	1865	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_009909185.1	s__Paenibacillus_Z glycinis	76.7037	169	1865	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_000722545.1	s__Paenibacillus_G tyrfis	76.6416	124	1865	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_017874275.1	s__Paenibacillus_Z sepulcri	76.6408	169	1865	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_907165215.1	s__Thermobacillus xylanilyticus	76.4319	155	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:47,906] [INFO] GTDB search result was written to GCF_003233845.1_ASM323384v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:47,906] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:47,910] [INFO] DFAST_QC result json was written to GCF_003233845.1_ASM323384v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:47,910] [INFO] DFAST_QC completed!
[2024-01-25 20:23:47,910] [INFO] Total running time: 0h1m57s