[2024-01-25 18:56:50,434] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:50,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:50,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference
[2024-01-25 18:56:51,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:51,589] [INFO] Task started: Prodigal
[2024-01-25 18:56:51,590] [INFO] Running command: gunzip -c /var/lib/cwl/stg41000bdc-3b99-4e2b-8bdd-8039712532d5/GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/cds.fna -a GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:10,605] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:10,606] [INFO] Task started: HMMsearch
[2024-01-25 18:57:10,606] [INFO] Running command: hmmsearch --tblout GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference/reference_markers.hmm GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:10,896] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:10,897] [INFO] Found 6/6 markers.
[2024-01-25 18:57:10,959] [INFO] Query marker FASTA was written to GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:57:10,960] [INFO] Task started: Blastn
[2024-01-25 18:57:10,960] [INFO] Running command: blastn -query GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference/reference_markers.fasta -out GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:11,505] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:11,507] [INFO] Selected 14 target genomes.
[2024-01-25 18:57:11,508] [INFO] Target genome list was writen to GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:57:11,540] [INFO] Task started: fastANI
[2024-01-25 18:57:11,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg41000bdc-3b99-4e2b-8bdd-8039712532d5/GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna.gz --refList GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:29,635] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:29,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:29,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:29,650] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:29,650] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:29,651] [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 polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	100.0	2146	2148	95	conclusive
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	84.1576	1621	2148	95	below_threshold
Paenibacillus barcinonensis	strain=CECT 7022	GCA_003217495.1	198119	198119	type	True	83.846	1513	2148	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	81.6207	1221	2148	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	81.5489	1225	2148	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	81.0793	1012	2148	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	80.9678	941	2148	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	80.964	958	2148	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	80.877	1028	2148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:29,652] [INFO] DFAST Taxonomy check result was written to GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:57:29,653] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:29,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:29,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference/checkm_data
[2024-01-25 18:57:29,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:29,725] [INFO] Task started: CheckM
[2024-01-25 18:57:29,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/checkm_input GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:58:26,287] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:26,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:26,308] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:26,309] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:26,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:58:26,310] [INFO] Task started: Blastn
[2024-01-25 18:58:26,310] [INFO] Running command: blastn -query GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f1d689d-e743-46ed-892e-5ad97ed56b33/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:27,101] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:27,104] [INFO] Selected 7 target genomes.
[2024-01-25 18:58:27,104] [INFO] Target genome list was writen to GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:27,112] [INFO] Task started: fastANI
[2024-01-25 18:58:27,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg41000bdc-3b99-4e2b-8bdd-8039712532d5/GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna.gz --refList GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:38,461] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:38,468] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:38,468] [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_900102085.1	s__Paenibacillus polysaccharolyticus	100.0	2146	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.73	97.72	0.92	0.92	4	conclusive
GCF_007680605.1	s__Paenibacillus xylanexedens_B	93.8547	1927	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.13	99.13	0.96	0.96	2	-
GCF_003719335.1	s__Paenibacillus amylolyticus_D	92.8703	1887	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512705.1	s__Paenibacillus sp017512705	84.416	1324	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639235.1	s__Paenibacillus silvae	84.1499	1623	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_003217495.1	s__Paenibacillus barcinonensis	83.8443	1513	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001955855.1	s__Paenibacillus sp001955855	81.4728	1220	2148	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.7262	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:38,471] [INFO] GTDB search result was written to GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:38,472] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:38,475] [INFO] DFAST_QC result json was written to GCF_900102085.1_IMG-taxon_2654588110_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:58:38,475] [INFO] DFAST_QC completed!
[2024-01-25 18:58:38,475] [INFO] Total running time: 0h1m48s