[2024-01-25 19:03:50,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:50,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:50,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference
[2024-01-25 19:03:51,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:51,882] [INFO] Task started: Prodigal
[2024-01-25 19:03:51,883] [INFO] Running command: gunzip -c /var/lib/cwl/stga5286607-11cb-412f-ae4b-822a5806f67a/GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/cds.fna -a GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:08,764] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:08,765] [INFO] Task started: HMMsearch
[2024-01-25 19:04:08,765] [INFO] Running command: hmmsearch --tblout GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference/reference_markers.hmm GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:09,161] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:09,162] [INFO] Found 6/6 markers.
[2024-01-25 19:04:09,214] [INFO] Query marker FASTA was written to GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:04:09,215] [INFO] Task started: Blastn
[2024-01-25 19:04:09,215] [INFO] Running command: blastn -query GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference/reference_markers.fasta -out GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:09,858] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:09,863] [INFO] Selected 14 target genomes.
[2024-01-25 19:04:09,863] [INFO] Target genome list was writen to GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:04:09,876] [INFO] Task started: fastANI
[2024-01-25 19:04:09,876] [INFO] Running command: fastANI --query /var/lib/cwl/stga5286607-11cb-412f-ae4b-822a5806f67a/GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna.gz --refList GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:27,159] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:27,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:27,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:27,170] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:27,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:27,170] [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 tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	100.0	1949	1957	95	conclusive
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	91.621	1583	1957	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	91.1027	1513	1957	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	90.6152	1448	1957	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	78.6859	453	1957	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	78.6188	407	1957	95	below_threshold
Paenibacillus naphthalenovorans	strain=PR-N1	GCA_900099895.1	162209	162209	type	True	78.5138	377	1957	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.8223	365	1957	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	77.3191	292	1957	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.9484	143	1957	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.8302	178	1957	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.73	218	1957	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.5143	164	1957	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	75.7875	84	1957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:27,171] [INFO] DFAST Taxonomy check result was written to GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:04:27,172] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:27,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:27,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference/checkm_data
[2024-01-25 19:04:27,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:27,230] [INFO] Task started: CheckM
[2024-01-25 19:04:27,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/checkm_input GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:05:15,161] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:15,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:15,180] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:15,180] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:15,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:05:15,181] [INFO] Task started: Blastn
[2024-01-25 19:05:15,181] [INFO] Running command: blastn -query GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ef9363e-e2a1-4eea-95b9-1bfdff16f792/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:16,008] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:16,010] [INFO] Selected 6 target genomes.
[2024-01-25 19:05:16,010] [INFO] Target genome list was writen to GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:16,017] [INFO] Task started: fastANI
[2024-01-25 19:05:16,017] [INFO] Running command: fastANI --query /var/lib/cwl/stga5286607-11cb-412f-ae4b-822a5806f67a/GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna.gz --refList GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:26,546] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:26,553] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:26,553] [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_900100345.1	s__Paenibacillus_G tianmuensis	100.0	1949	1957	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	conclusive
GCF_001399685.1	s__Paenibacillus_G sp001399685	91.7029	1433	1957	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_000722545.1	s__Paenibacillus_G tyrfis	91.6375	1581	1957	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_018998565.1	s__Paenibacillus_G sp018998565	91.5431	1513	1957	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_004000865.1	s__Paenibacillus_G elgii	91.1106	1513	1957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	90.6178	1448	1957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:26,554] [INFO] GTDB search result was written to GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:26,555] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:26,557] [INFO] DFAST_QC result json was written to GCF_900100345.1_IMG-taxon_2617270934_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:05:26,558] [INFO] DFAST_QC completed!
[2024-01-25 19:05:26,558] [INFO] Total running time: 0h1m36s