[2024-01-24 13:01:19,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference
[2024-01-24 13:01:21,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:21,126] [INFO] Task started: Prodigal
[2024-01-24 13:01:21,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg35772096-37c6-49a8-8b2e-fe79df59453c/GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/cds.fna -a GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:28,277] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:28,278] [INFO] Task started: HMMsearch
[2024-01-24 13:01:28,278] [INFO] Running command: hmmsearch --tblout GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference/reference_markers.hmm GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:28,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:28,545] [INFO] Found 6/6 markers.
[2024-01-24 13:01:28,576] [INFO] Query marker FASTA was written to GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:28,577] [INFO] Task started: Blastn
[2024-01-24 13:01:28,577] [INFO] Running command: blastn -query GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference/reference_markers.fasta -out GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:29,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:29,249] [INFO] Selected 23 target genomes.
[2024-01-24 13:01:29,250] [INFO] Target genome list was writen to GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:29,263] [INFO] Task started: fastANI
[2024-01-24 13:01:29,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg35772096-37c6-49a8-8b2e-fe79df59453c/GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna.gz --refList GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:42,370] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:42,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:42,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:42,375] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:42,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:42,375] [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
Acetanaerobacterium elongatum	strain=CGMCC 1.5012	GCA_900103835.1	258515	258515	type	True	100.0	928	935	95	conclusive
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.8514	60	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:42,377] [INFO] DFAST Taxonomy check result was written to GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:42,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:42,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:42,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference/checkm_data
[2024-01-24 13:01:42,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:42,409] [INFO] Task started: CheckM
[2024-01-24 13:01:42,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/checkm_input GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:08,616] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:08,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:08,643] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:08,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:08,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:08,644] [INFO] Task started: Blastn
[2024-01-24 13:02:08,645] [INFO] Running command: blastn -query GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdebdd1c8-4afb-4b63-989f-675cb7991b6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:09,682] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:09,685] [INFO] Selected 28 target genomes.
[2024-01-24 13:02:09,685] [INFO] Target genome list was writen to GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:09,739] [INFO] Task started: fastANI
[2024-01-24 13:02:09,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg35772096-37c6-49a8-8b2e-fe79df59453c/GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna.gz --refList GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:20,391] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:20,398] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:20,398] [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_900103835.1	s__Acetanaerobacterium elongatum	100.0	928	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Acetanaerobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014384885.1	s__Hydrogenoanaerobacterium sp014384885	76.8514	60	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,400] [INFO] GTDB search result was written to GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:20,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:20,402] [INFO] DFAST_QC result json was written to GCF_900103835.1_IMG-taxon_2667527408_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:20,402] [INFO] DFAST_QC completed!
[2024-01-24 13:02:20,403] [INFO] Total running time: 0h1m1s