[2024-01-25 20:18:20,858] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:20,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:20,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference
[2024-01-25 20:18:22,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,021] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,021] [INFO] Running command: gunzip -c /var/lib/cwl/stgea8cdd82-2aeb-45c5-a153-34249fa4b479/GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/cds.fna -a GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:37,964] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:37,964] [INFO] Task started: HMMsearch
[2024-01-25 20:18:37,964] [INFO] Running command: hmmsearch --tblout GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference/reference_markers.hmm GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:38,243] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:38,244] [INFO] Found 6/6 markers.
[2024-01-25 20:18:38,282] [INFO] Query marker FASTA was written to GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:18:38,282] [INFO] Task started: Blastn
[2024-01-25 20:18:38,282] [INFO] Running command: blastn -query GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference/reference_markers.fasta -out GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:38,833] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:38,837] [INFO] Selected 23 target genomes.
[2024-01-25 20:18:38,837] [INFO] Target genome list was writen to GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:18:38,858] [INFO] Task started: fastANI
[2024-01-25 20:18:38,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgea8cdd82-2aeb-45c5-a153-34249fa4b479/GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna.gz --refList GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:01,000] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:01,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:01,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:01,005] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:01,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:01,006] [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
Arachidicoccus rhizosphaerae	strain=Vu-144	GCA_900107765.1	551991	551991	type	True	100.0	1592	1592	95	conclusive
Arachidicoccus ginsenosidivorans	strain=Gsoil 809	GCA_007971385.1	496057	496057	type	True	79.9379	641	1592	95	below_threshold
Arachidicoccus terrestris	strain=5GH13-10	GCA_020042345.1	2875539	2875539	type	True	78.9642	515	1592	95	below_threshold
Arachidicoccus soli	strain=KIS59-12	GCA_003600625.1	2341117	2341117	type	True	76.9609	90	1592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:01,007] [INFO] DFAST Taxonomy check result was written to GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:19:01,008] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:01,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:01,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference/checkm_data
[2024-01-25 20:19:01,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:01,056] [INFO] Task started: CheckM
[2024-01-25 20:19:01,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/checkm_input GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:19:47,670] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:47,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:47,691] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:47,691] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:47,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:19:47,692] [INFO] Task started: Blastn
[2024-01-25 20:19:47,692] [INFO] Running command: blastn -query GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg804e219a-c98d-4556-81ea-f564426746bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:48,498] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:48,503] [INFO] Selected 28 target genomes.
[2024-01-25 20:19:48,503] [INFO] Target genome list was writen to GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:48,536] [INFO] Task started: fastANI
[2024-01-25 20:19:48,536] [INFO] Running command: fastANI --query /var/lib/cwl/stgea8cdd82-2aeb-45c5-a153-34249fa4b479/GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna.gz --refList GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:11,563] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:11,568] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:11,569] [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_900107765.1	s__Arachidicoccus rhizosphaerae	100.0	1592	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007971385.1	s__Arachidicoccus ginsenosidivorans	79.9349	642	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600625.1	s__Arachidicoccus soli	76.8867	91	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097095.1	s__Filimonas sp003097095	76.2848	61	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659705.1	s__Arachidicoccus sp001659705	75.8579	63	1592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:11,571] [INFO] GTDB search result was written to GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:11,571] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:11,574] [INFO] DFAST_QC result json was written to GCF_900107765.1_IMG-taxon_2651870123_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:20:11,575] [INFO] DFAST_QC completed!
[2024-01-25 20:20:11,575] [INFO] Total running time: 0h1m51s