[2024-01-24 13:55:47,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:47,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:47,676] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference
[2024-01-24 13:55:49,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,074] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,074] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbbd425e-3424-4077-b1c3-7c80dab38702/GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/cds.fna -a GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:57,052] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:57,052] [INFO] Task started: HMMsearch
[2024-01-24 13:55:57,052] [INFO] Running command: hmmsearch --tblout GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference/reference_markers.hmm GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:57,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:57,313] [INFO] Found 6/6 markers.
[2024-01-24 13:55:57,339] [INFO] Query marker FASTA was written to GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:55:57,339] [INFO] Task started: Blastn
[2024-01-24 13:55:57,339] [INFO] Running command: blastn -query GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference/reference_markers.fasta -out GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:57,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:57,983] [INFO] Selected 24 target genomes.
[2024-01-24 13:55:57,984] [INFO] Target genome list was writen to GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:55:58,004] [INFO] Task started: fastANI
[2024-01-24 13:55:58,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbd425e-3424-4077-b1c3-7c80dab38702/GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna.gz --refList GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:12,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:12,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:12,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:12,136] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:12,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:12,136] [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
Thermoclostridium caenicola	strain=DSM 19027	GCA_900142095.1	659425	659425	type	True	100.0	891	896	95	conclusive
Thermoclostridium stercorarium subsp. leptospartum	strain=DSM 9219	GCA_001697285.1	160385	1510	type	True	85.1917	61	896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:12,138] [INFO] DFAST Taxonomy check result was written to GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:56:12,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:12,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:12,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference/checkm_data
[2024-01-24 13:56:12,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:12,175] [INFO] Task started: CheckM
[2024-01-24 13:56:12,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/checkm_input GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:56:40,602] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:40,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:40,618] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:40,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:40,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:56:40,620] [INFO] Task started: Blastn
[2024-01-24 13:56:40,620] [INFO] Running command: blastn -query GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe5f0be4-99e0-43b5-9991-1efae9131126/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:41,742] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:41,746] [INFO] Selected 15 target genomes.
[2024-01-24 13:56:41,746] [INFO] Target genome list was writen to GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:41,771] [INFO] Task started: fastANI
[2024-01-24 13:56:41,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbd425e-3424-4077-b1c3-7c80dab38702/GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna.gz --refList GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:48,607] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:48,619] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:48,619] [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_900142095.1	s__Thermoclostridium_A caenicola	100.0	891	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012719645.1	s__Thermoclostridium_A sp012719645	78.8384	427	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001512555.1	s__Thermoclostridium_A sp001512555	78.7657	354	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	99.53	99.53	0.85	0.85	2	-
GCA_012518025.1	s__Thermoclostridium_A sp012518025	78.6957	314	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728015.1	s__Thermoclostridium_A sp012728015	78.4964	366	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719545.1	s__DTU059 sp012719545	76.6181	58	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376415.1	s__DTU059 sp002376415	76.4149	96	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:48,621] [INFO] GTDB search result was written to GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:48,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:48,624] [INFO] DFAST_QC result json was written to GCF_900142095.1_IMG-taxon_2700988698_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:56:48,624] [INFO] DFAST_QC completed!
[2024-01-24 13:56:48,624] [INFO] Total running time: 0h1m1s