[2024-01-24 13:40:29,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:29,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:29,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference
[2024-01-24 13:40:31,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,206] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,206] [INFO] Running command: gunzip -c /var/lib/cwl/stge9794ade-f7de-43b0-927e-8836c31e5536/GCF_004001025.1_ASM400102v1_genomic.fna.gz | prodigal -d GCF_004001025.1_ASM400102v1_genomic.fna/cds.fna -a GCF_004001025.1_ASM400102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:51,463] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:51,464] [INFO] Task started: HMMsearch
[2024-01-24 13:40:51,464] [INFO] Running command: hmmsearch --tblout GCF_004001025.1_ASM400102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference/reference_markers.hmm GCF_004001025.1_ASM400102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,843] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,902] [INFO] Query marker FASTA was written to GCF_004001025.1_ASM400102v1_genomic.fna/markers.fasta
[2024-01-24 13:40:51,902] [INFO] Task started: Blastn
[2024-01-24 13:40:51,903] [INFO] Running command: blastn -query GCF_004001025.1_ASM400102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference/reference_markers.fasta -out GCF_004001025.1_ASM400102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,535] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,538] [INFO] Selected 9 target genomes.
[2024-01-24 13:40:52,538] [INFO] Target genome list was writen to GCF_004001025.1_ASM400102v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,548] [INFO] Task started: fastANI
[2024-01-24 13:40:52,548] [INFO] Running command: fastANI --query /var/lib/cwl/stge9794ade-f7de-43b0-927e-8836c31e5536/GCF_004001025.1_ASM400102v1_genomic.fna.gz --refList GCF_004001025.1_ASM400102v1_genomic.fna/target_genomes.txt --output GCF_004001025.1_ASM400102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:07,834] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:07,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:07,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:07,846] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:07,846] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:41:07,846] [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 amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	100.0	2331	2336	95	inconclusive
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	96.078	2011	2336	95	inconclusive
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	83.5732	1519	2336	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	83.5268	1512	2336	95	below_threshold
Paenibacillus xylanivorans	strain=A59	GCA_001280595.1	1705561	1705561	type	True	83.5093	1468	2336	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	82.4737	1302	2336	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	82.2428	1269	2336	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	81.5091	1237	2336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:07,853] [INFO] DFAST Taxonomy check result was written to GCF_004001025.1_ASM400102v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:07,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:07,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:07,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference/checkm_data
[2024-01-24 13:41:07,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:07,924] [INFO] Task started: CheckM
[2024-01-24 13:41:07,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004001025.1_ASM400102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004001025.1_ASM400102v1_genomic.fna/checkm_input GCF_004001025.1_ASM400102v1_genomic.fna/checkm_result
[2024-01-24 13:42:10,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:10,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:10,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:10,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004001025.1_ASM400102v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:10,257] [INFO] Task started: Blastn
[2024-01-24 13:42:10,257] [INFO] Running command: blastn -query GCF_004001025.1_ASM400102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6da5d01d-508d-483f-8a77-2269cb7ae137/dqc_reference/reference_markers_gtdb.fasta -out GCF_004001025.1_ASM400102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:11,032] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:11,035] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:11,035] [INFO] Target genome list was writen to GCF_004001025.1_ASM400102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:11,059] [INFO] Task started: fastANI
[2024-01-24 13:42:11,059] [INFO] Running command: fastANI --query /var/lib/cwl/stge9794ade-f7de-43b0-927e-8836c31e5536/GCF_004001025.1_ASM400102v1_genomic.fna.gz --refList GCF_004001025.1_ASM400102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004001025.1_ASM400102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:29,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:29,022] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:29,023] [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_004001025.1	s__Paenibacillus amylolyticus	100.0	2331	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	97.25	97.08	0.90	0.88	9	conclusive
GCF_001908275.1	s__Paenibacillus xylanexedens_A	96.2155	2053	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	N/A	N/A	N/A	N/A	1	conclusive
GCF_017874615.1	s__Paenibacillus xylanexedens	96.078	2011	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.078	N/A	N/A	N/A	N/A	1	conclusive
GCF_001955855.1	s__Paenibacillus sp001955855	95.6573	1980	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.7262	N/A	N/A	N/A	N/A	1	-
GCF_000316035.1	s__Paenibacillus sp000316035	95.3036	1922	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.8348	N/A	N/A	N/A	N/A	1	-
GCF_900101225.1	s__Paenibacillus sp900101225	95.1685	2036	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.22	98.17	98.17	0.94	0.94	2	-
GCF_008386395.1	s__Paenibacillus amylolyticus_B	94.7621	2034	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.96	95.65	0.92	0.85	8	-
GCF_018614975.1	s__Paenibacillus polymyxa_E	94.2258	1841	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514495.1	s__Paenibacillus pabuli	83.5738	1518	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287275.1	s__Paenibacillus taichungensis_A	83.5013	1464	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217495.1	s__Paenibacillus barcinonensis	81.4398	1132	2336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,024] [INFO] GTDB search result was written to GCF_004001025.1_ASM400102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:29,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:29,028] [INFO] DFAST_QC result json was written to GCF_004001025.1_ASM400102v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:29,028] [INFO] DFAST_QC completed!
[2024-01-24 13:42:29,028] [INFO] Total running time: 0h1m59s