[2024-01-24 14:39:15,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,235] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference
[2024-01-24 14:39:16,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,587] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,587] [INFO] Running command: gunzip -c /var/lib/cwl/stge9fb5f65-12bb-4ff5-99d7-9fa487f99844/GCF_017874615.1_ASM1787461v1_genomic.fna.gz | prodigal -d GCF_017874615.1_ASM1787461v1_genomic.fna/cds.fna -a GCF_017874615.1_ASM1787461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:40,072] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:40,072] [INFO] Task started: HMMsearch
[2024-01-24 14:39:40,072] [INFO] Running command: hmmsearch --tblout GCF_017874615.1_ASM1787461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference/reference_markers.hmm GCF_017874615.1_ASM1787461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:40,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:40,418] [INFO] Found 6/6 markers.
[2024-01-24 14:39:40,480] [INFO] Query marker FASTA was written to GCF_017874615.1_ASM1787461v1_genomic.fna/markers.fasta
[2024-01-24 14:39:40,480] [INFO] Task started: Blastn
[2024-01-24 14:39:40,480] [INFO] Running command: blastn -query GCF_017874615.1_ASM1787461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference/reference_markers.fasta -out GCF_017874615.1_ASM1787461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:41,095] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:41,099] [INFO] Selected 9 target genomes.
[2024-01-24 14:39:41,100] [INFO] Target genome list was writen to GCF_017874615.1_ASM1787461v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:41,104] [INFO] Task started: fastANI
[2024-01-24 14:39:41,104] [INFO] Running command: fastANI --query /var/lib/cwl/stge9fb5f65-12bb-4ff5-99d7-9fa487f99844/GCF_017874615.1_ASM1787461v1_genomic.fna.gz --refList GCF_017874615.1_ASM1787461v1_genomic.fna/target_genomes.txt --output GCF_017874615.1_ASM1787461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:55,684] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:55,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:55,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:55,692] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:55,692] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:39:55,692] [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 xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	100.0	2302	2302	95	inconclusive
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	96.0662	1985	2302	95	inconclusive
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	83.6207	1500	2302	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	83.5706	1506	2302	95	below_threshold
Paenibacillus xylanivorans	strain=A59	GCA_001280595.1	1705561	1705561	type	True	83.4632	1446	2302	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	82.4831	1269	2302	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	82.1534	1248	2302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:55,694] [INFO] DFAST Taxonomy check result was written to GCF_017874615.1_ASM1787461v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:55,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:55,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:55,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference/checkm_data
[2024-01-24 14:39:55,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:55,760] [INFO] Task started: CheckM
[2024-01-24 14:39:55,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874615.1_ASM1787461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874615.1_ASM1787461v1_genomic.fna/checkm_input GCF_017874615.1_ASM1787461v1_genomic.fna/checkm_result
[2024-01-24 14:41:03,374] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:03,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:03,399] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:03,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:03,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874615.1_ASM1787461v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:03,400] [INFO] Task started: Blastn
[2024-01-24 14:41:03,400] [INFO] Running command: blastn -query GCF_017874615.1_ASM1787461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12dc238-2d0e-40a3-96b3-6569543793c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874615.1_ASM1787461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:04,150] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:04,154] [INFO] Selected 9 target genomes.
[2024-01-24 14:41:04,155] [INFO] Target genome list was writen to GCF_017874615.1_ASM1787461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:04,162] [INFO] Task started: fastANI
[2024-01-24 14:41:04,162] [INFO] Running command: fastANI --query /var/lib/cwl/stge9fb5f65-12bb-4ff5-99d7-9fa487f99844/GCF_017874615.1_ASM1787461v1_genomic.fna.gz --refList GCF_017874615.1_ASM1787461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874615.1_ASM1787461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:19,604] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:19,613] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:19,613] [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_017874615.1	s__Paenibacillus xylanexedens	100.0	2302	2302	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_004001025.1	s__Paenibacillus amylolyticus	96.07	1984	2302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	97.25	97.08	0.90	0.88	9	-
GCF_001908275.1	s__Paenibacillus xylanexedens_A	95.8628	2082	2302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	N/A	N/A	N/A	N/A	1	-
GCF_000316035.1	s__Paenibacillus sp000316035	95.791	1968	2302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.8348	N/A	N/A	N/A	N/A	1	-
GCF_001955855.1	s__Paenibacillus sp001955855	95.2824	1958	2302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.7262	N/A	N/A	N/A	N/A	1	-
GCF_900101225.1	s__Paenibacillus sp900101225	94.9977	1973	2302	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	94.6038	1999	2302	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	94.2878	1838	2302	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	83.5626	1475	2302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:19,615] [INFO] GTDB search result was written to GCF_017874615.1_ASM1787461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:19,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:19,621] [INFO] DFAST_QC result json was written to GCF_017874615.1_ASM1787461v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:19,622] [INFO] DFAST_QC completed!
[2024-01-24 14:41:19,622] [INFO] Total running time: 0h2m4s