[2023-06-13 11:16:29,603] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:16:29,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:16:29,609] [INFO] DQC Reference Directory: /var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference
[2023-06-13 11:16:30,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:16:30,909] [INFO] Task started: Prodigal
[2023-06-13 11:16:30,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg15352744-cee5-4c79-8ef4-024ba1b82e04/GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna.gz | prodigal -d GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/cds.fna -a GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:16:34,943] [INFO] Task succeeded: Prodigal
[2023-06-13 11:16:34,943] [INFO] Task started: HMMsearch
[2023-06-13 11:16:34,943] [INFO] Running command: hmmsearch --tblout GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference/reference_markers.hmm GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:16:35,220] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:16:35,221] [INFO] Found 6/6 markers.
[2023-06-13 11:16:35,242] [INFO] Query marker FASTA was written to GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/markers.fasta
[2023-06-13 11:16:35,242] [INFO] Task started: Blastn
[2023-06-13 11:16:35,242] [INFO] Running command: blastn -query GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference/reference_markers.fasta -out GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:16:35,887] [INFO] Task succeeded: Blastn
[2023-06-13 11:16:35,893] [INFO] Selected 30 target genomes.
[2023-06-13 11:16:35,893] [INFO] Target genome list was writen to GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/target_genomes.txt
[2023-06-13 11:16:35,900] [INFO] Task started: fastANI
[2023-06-13 11:16:35,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg15352744-cee5-4c79-8ef4-024ba1b82e04/GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna.gz --refList GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/target_genomes.txt --output GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:16:54,744] [INFO] Task succeeded: fastANI
[2023-06-13 11:16:54,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:16:54,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:16:54,749] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:16:54,749] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 11:16:54,749] [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
--------------------------------------------------------------------------------
[2023-06-13 11:16:54,752] [INFO] DFAST Taxonomy check result was written to GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/tc_result.tsv
[2023-06-13 11:16:54,753] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:16:54,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:16:54,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference/checkm_data
[2023-06-13 11:16:54,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:16:54,787] [INFO] Task started: CheckM
[2023-06-13 11:16:54,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/checkm_input GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/checkm_result
[2023-06-13 11:17:13,906] [INFO] Task succeeded: CheckM
[2023-06-13 11:17:13,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:17:13,932] [INFO] ===== Completeness check finished =====
[2023-06-13 11:17:13,932] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:17:13,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/markers.fasta)
[2023-06-13 11:17:13,933] [INFO] Task started: Blastn
[2023-06-13 11:17:13,933] [INFO] Running command: blastn -query GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0935720-bf2d-414b-9520-f42af88cae45/dqc_reference/reference_markers_gtdb.fasta -out GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:17:14,927] [INFO] Task succeeded: Blastn
[2023-06-13 11:17:14,932] [INFO] Selected 25 target genomes.
[2023-06-13 11:17:14,933] [INFO] Target genome list was writen to GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:17:14,948] [INFO] Task started: fastANI
[2023-06-13 11:17:14,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg15352744-cee5-4c79-8ef4-024ba1b82e04/GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna.gz --refList GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:17:29,137] [INFO] Task succeeded: fastANI
[2023-06-13 11:17:29,146] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:17:29,146] [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
GCA_018699395.1	s__UBA1847 sp018699395	98.4784	385	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009937445.1	s__UBA1847 sp009937445	77.1129	101	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338605.1	s__UBA1847 sp002338605	76.9315	54	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:17:29,151] [INFO] GTDB search result was written to GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:17:29,154] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:17:29,157] [INFO] DFAST_QC result json was written to GCA_938083435.1_S2_Bin_METABAT_225_1_genomic.fna/dqc_result.json
[2023-06-13 11:17:29,158] [INFO] DFAST_QC completed!
[2023-06-13 11:17:29,158] [INFO] Total running time: 0h0m60s