[2024-01-24 13:45:45,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference
[2024-01-24 13:45:47,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,283] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg23ae1fce-e89b-42c5-9fd8-65eb73ed028e/GCF_000020945.1_ASM2094v1_genomic.fna.gz | prodigal -d GCF_000020945.1_ASM2094v1_genomic.fna/cds.fna -a GCF_000020945.1_ASM2094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:51,221] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:51,221] [INFO] Task started: HMMsearch
[2024-01-24 13:45:51,221] [INFO] Running command: hmmsearch --tblout GCF_000020945.1_ASM2094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference/reference_markers.hmm GCF_000020945.1_ASM2094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:51,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:51,500] [INFO] Found 6/6 markers.
[2024-01-24 13:45:51,519] [INFO] Query marker FASTA was written to GCF_000020945.1_ASM2094v1_genomic.fna/markers.fasta
[2024-01-24 13:45:51,520] [INFO] Task started: Blastn
[2024-01-24 13:45:51,520] [INFO] Running command: blastn -query GCF_000020945.1_ASM2094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference/reference_markers.fasta -out GCF_000020945.1_ASM2094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:52,124] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:52,128] [INFO] Selected 9 target genomes.
[2024-01-24 13:45:52,129] [INFO] Target genome list was writen to GCF_000020945.1_ASM2094v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:52,135] [INFO] Task started: fastANI
[2024-01-24 13:45:52,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg23ae1fce-e89b-42c5-9fd8-65eb73ed028e/GCF_000020945.1_ASM2094v1_genomic.fna.gz --refList GCF_000020945.1_ASM2094v1_genomic.fna/target_genomes.txt --output GCF_000020945.1_ASM2094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:45:56,943] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:56,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:45:56,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:45:56,953] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:45:56,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:45:56,954] [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
Coprothermobacter proteolyticus	strain=DSM 5265	GCA_000020945.1	35786	35786	type	True	100.0	474	474	95	conclusive
Coprothermobacter platensis	strain=DSM 11748	GCA_000378005.1	108819	108819	type	True	78.2846	67	474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:45:56,957] [INFO] DFAST Taxonomy check result was written to GCF_000020945.1_ASM2094v1_genomic.fna/tc_result.tsv
[2024-01-24 13:45:56,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:45:56,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:45:56,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference/checkm_data
[2024-01-24 13:45:56,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:45:56,993] [INFO] Task started: CheckM
[2024-01-24 13:45:56,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020945.1_ASM2094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020945.1_ASM2094v1_genomic.fna/checkm_input GCF_000020945.1_ASM2094v1_genomic.fna/checkm_result
[2024-01-24 13:46:16,051] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:16,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:16,075] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:16,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:16,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020945.1_ASM2094v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:16,077] [INFO] Task started: Blastn
[2024-01-24 13:46:16,077] [INFO] Running command: blastn -query GCF_000020945.1_ASM2094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16dec23a-ad8b-45e9-908c-fe87f14bb0ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020945.1_ASM2094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:17,187] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:17,204] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:17,205] [INFO] Target genome list was writen to GCF_000020945.1_ASM2094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:17,225] [INFO] Task started: fastANI
[2024-01-24 13:46:17,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg23ae1fce-e89b-42c5-9fd8-65eb73ed028e/GCF_000020945.1_ASM2094v1_genomic.fna.gz --refList GCF_000020945.1_ASM2094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020945.1_ASM2094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:21,475] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:21,480] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:21,480] [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_000020945.1	s__Coprothermobacter proteolyticus	100.0	474	474	d__Bacteria;p__Coprothermobacterota;c__Coprothermobacteria;o__Coprothermobacterales;f__Coprothermobacteraceae;g__Coprothermobacter	95.0	97.78	97.43	0.90	0.79	6	conclusive
GCA_003476705.1	s__Coprothermobacter sp003476705	92.7932	289	474	d__Bacteria;p__Coprothermobacterota;c__Coprothermobacteria;o__Coprothermobacterales;f__Coprothermobacteraceae;g__Coprothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842545.1	s__Coprothermobacter sp012842545	81.5858	171	474	d__Bacteria;p__Coprothermobacterota;c__Coprothermobacteria;o__Coprothermobacterales;f__Coprothermobacteraceae;g__Coprothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378005.1	s__Coprothermobacter platensis	78.0213	66	474	d__Bacteria;p__Coprothermobacterota;c__Coprothermobacteria;o__Coprothermobacterales;f__Coprothermobacteraceae;g__Coprothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:21,482] [INFO] GTDB search result was written to GCF_000020945.1_ASM2094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:21,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:21,486] [INFO] DFAST_QC result json was written to GCF_000020945.1_ASM2094v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:21,486] [INFO] DFAST_QC completed!
[2024-01-24 13:46:21,486] [INFO] Total running time: 0h0m36s