[2024-01-24 14:12:47,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference
[2024-01-24 14:12:48,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,682] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,682] [INFO] Running command: gunzip -c /var/lib/cwl/stgf111b5db-3f78-4b48-a77b-2ead8314eb85/GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/cds.fna -a GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:53,963] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:53,963] [INFO] Task started: HMMsearch
[2024-01-24 14:12:53,963] [INFO] Running command: hmmsearch --tblout GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference/reference_markers.hmm GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:54,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:54,198] [INFO] Found 6/6 markers.
[2024-01-24 14:12:54,228] [INFO] Query marker FASTA was written to GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:54,229] [INFO] Task started: Blastn
[2024-01-24 14:12:54,229] [INFO] Running command: blastn -query GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference/reference_markers.fasta -out GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:54,802] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:54,806] [INFO] Selected 19 target genomes.
[2024-01-24 14:12:54,807] [INFO] Target genome list was writen to GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:54,816] [INFO] Task started: fastANI
[2024-01-24 14:12:54,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgf111b5db-3f78-4b48-a77b-2ead8314eb85/GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna.gz --refList GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:02,729] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:02,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:02,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:02,740] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:02,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:02,740] [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
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	78.0336	166	982	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	77.8811	170	982	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	76.4791	120	982	95	below_threshold
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	76.3747	96	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:02,742] [INFO] DFAST Taxonomy check result was written to GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:13:02,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:02,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:02,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference/checkm_data
[2024-01-24 14:13:02,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:02,777] [INFO] Task started: CheckM
[2024-01-24 14:13:02,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/checkm_input GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:25,413] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:25,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,436] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:25,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:25,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:25,438] [INFO] Task started: Blastn
[2024-01-24 14:13:25,438] [INFO] Running command: blastn -query GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg56c14f6c-522f-4ec4-8d89-3b15dd2baad4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:26,224] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:26,228] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:26,228] [INFO] Target genome list was writen to GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:26,238] [INFO] Task started: fastANI
[2024-01-24 14:13:26,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgf111b5db-3f78-4b48-a77b-2ead8314eb85/GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna.gz --refList GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:32,028] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:32,042] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:32,042] [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_900106765.1	s__Tepidimicrobium xylanilyticum	100.0	979	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Tepidimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012728595.1	s__Tepidimicrobium sp012728595	81.1822	416	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Tepidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511955.1	s__Schnuerera ultunensis	78.5054	339	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Schnuerera	95.0	99.51	99.51	0.99	0.99	2	-
GCA_012728725.1	s__JAAYEM01 sp012728725	77.5241	171	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAYEM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902386935.1	s__CABMKH01 sp902386935	77.4575	59	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__CABMKH01	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001282665.1	s__Mt11 sp001282665	77.3782	206	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Mt11	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012735405.1	s__JAAYFE01 sp012735405	76.772	128	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAYFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728075.1	s__Keratinibaculum sp012728075	76.6346	147	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799055.1	s__JAAZMA01 sp012799055	76.5704	113	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798935.1	s__JAAZMG01 sp012798935	76.5647	114	982	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:32,044] [INFO] GTDB search result was written to GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:32,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:32,047] [INFO] DFAST_QC result json was written to GCF_900106765.1_IMG-taxon_2599185171_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:32,047] [INFO] DFAST_QC completed!
[2024-01-24 14:13:32,048] [INFO] Total running time: 0h0m45s