[2024-01-24 12:30:05,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference
[2024-01-24 12:30:07,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,248] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg1613e922-755c-46b6-924e-337bb9521193/GCF_014779765.1_ASM1477976v1_genomic.fna.gz | prodigal -d GCF_014779765.1_ASM1477976v1_genomic.fna/cds.fna -a GCF_014779765.1_ASM1477976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:23,976] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:23,976] [INFO] Task started: HMMsearch
[2024-01-24 12:30:23,976] [INFO] Running command: hmmsearch --tblout GCF_014779765.1_ASM1477976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference/reference_markers.hmm GCF_014779765.1_ASM1477976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:24,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:24,286] [INFO] Found 6/6 markers.
[2024-01-24 12:30:24,336] [INFO] Query marker FASTA was written to GCF_014779765.1_ASM1477976v1_genomic.fna/markers.fasta
[2024-01-24 12:30:24,336] [INFO] Task started: Blastn
[2024-01-24 12:30:24,337] [INFO] Running command: blastn -query GCF_014779765.1_ASM1477976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference/reference_markers.fasta -out GCF_014779765.1_ASM1477976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:24,893] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:24,896] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:24,896] [INFO] Target genome list was writen to GCF_014779765.1_ASM1477976v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:24,900] [INFO] Task started: fastANI
[2024-01-24 12:30:24,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg1613e922-755c-46b6-924e-337bb9521193/GCF_014779765.1_ASM1477976v1_genomic.fna.gz --refList GCF_014779765.1_ASM1477976v1_genomic.fna/target_genomes.txt --output GCF_014779765.1_ASM1477976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:42,535] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:42,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:42,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:42,547] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:42,547] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:42,547] [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 cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	84.5824	1505	2249	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	79.8055	720	2249	95	below_threshold
Paenibacillus xylaniclasticus	strain=NBRC 106381	GCA_004001065.1	588083	588083	type	True	79.216	458	2249	95	below_threshold
Paenibacillus curdlanolyticus	strain=YK9	GCA_000179615.1	59840	59840	type	True	79.035	534	2249	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.9381	305	2249	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	77.6238	309	2249	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	77.4553	284	2249	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	77.3938	198	2249	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	77.1912	223	2249	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.1812	218	2249	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	77.05	87	2249	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.8287	163	2249	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.7033	176	2249	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.587	143	2249	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	76.5544	103	2249	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.276	88	2249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:42,548] [INFO] DFAST Taxonomy check result was written to GCF_014779765.1_ASM1477976v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:42,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:42,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:42,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference/checkm_data
[2024-01-24 12:30:42,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:42,615] [INFO] Task started: CheckM
[2024-01-24 12:30:42,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014779765.1_ASM1477976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014779765.1_ASM1477976v1_genomic.fna/checkm_input GCF_014779765.1_ASM1477976v1_genomic.fna/checkm_result
[2024-01-24 12:31:29,602] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:29,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:29,621] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:29,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:29,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014779765.1_ASM1477976v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:29,622] [INFO] Task started: Blastn
[2024-01-24 12:31:29,622] [INFO] Running command: blastn -query GCF_014779765.1_ASM1477976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9baadce3-b79e-4c45-969d-6b0a902f4061/dqc_reference/reference_markers_gtdb.fasta -out GCF_014779765.1_ASM1477976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:30,410] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:30,412] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:30,412] [INFO] Target genome list was writen to GCF_014779765.1_ASM1477976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:30,418] [INFO] Task started: fastANI
[2024-01-24 12:31:30,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg1613e922-755c-46b6-924e-337bb9521193/GCF_014779765.1_ASM1477976v1_genomic.fna.gz --refList GCF_014779765.1_ASM1477976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014779765.1_ASM1477976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:45,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:45,328] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:45,328] [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_014779765.1	s__Paenibacillus_T sp014779765	100.0	2247	2249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003182255.1	s__Paenibacillus_T cellulosilyticus	84.5776	1506	2249	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_004000825.1	s__Paenibacillus_T kobensis	79.8081	720	2249	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_004001065.1	s__Paenibacillus_T xylaniclasticus	79.2109	459	2249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000179615.1	s__Paenibacillus_T curdlanolyticus	79.0397	533	2249	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_009789195.1	s__Paenibacillus_T sp009789195	78.8389	501	2249	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_004345425.1	s__Paenibacillus_C sp004345425	77.5479	294	2249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	77.4661	283	2249	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_003583765.1	s__Paenibacillus_C nanensis	77.1912	223	2249	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_003268025.1	s__Paenibacillus_Z montanisoli	77.1812	218	2249	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_014705655.1	s__Paenibacillus_C sp014705655	77.0678	237	2249	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_900100345.1	s__Paenibacillus_G tianmuensis	76.5544	103	2249	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:45,329] [INFO] GTDB search result was written to GCF_014779765.1_ASM1477976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:45,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:45,333] [INFO] DFAST_QC result json was written to GCF_014779765.1_ASM1477976v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:45,333] [INFO] DFAST_QC completed!
[2024-01-24 12:31:45,333] [INFO] Total running time: 0h1m40s