[2023-06-12 22:40:34,336] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:40:34,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:40:34,341] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference
[2023-06-12 22:40:35,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:40:35,756] [INFO] Task started: Prodigal
[2023-06-12 22:40:35,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg1df2d4ae-24c9-4e04-96ca-d56de7f86a98/GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna.gz | prodigal -d GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/cds.fna -a GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:40:39,825] [INFO] Task succeeded: Prodigal
[2023-06-12 22:40:39,825] [INFO] Task started: HMMsearch
[2023-06-12 22:40:39,826] [INFO] Running command: hmmsearch --tblout GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference/reference_markers.hmm GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:40:40,058] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:40:40,059] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1df2d4ae-24c9-4e04-96ca-d56de7f86a98/GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna.gz]
[2023-06-12 22:40:40,089] [INFO] Query marker FASTA was written to GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/markers.fasta
[2023-06-12 22:40:40,090] [INFO] Task started: Blastn
[2023-06-12 22:40:40,090] [INFO] Running command: blastn -query GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference/reference_markers.fasta -out GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:40:40,668] [INFO] Task succeeded: Blastn
[2023-06-12 22:40:40,672] [INFO] Selected 16 target genomes.
[2023-06-12 22:40:40,673] [INFO] Target genome list was writen to GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/target_genomes.txt
[2023-06-12 22:40:40,701] [INFO] Task started: fastANI
[2023-06-12 22:40:40,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg1df2d4ae-24c9-4e04-96ca-d56de7f86a98/GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna.gz --refList GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/target_genomes.txt --output GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:40:49,765] [INFO] Task succeeded: fastANI
[2023-06-12 22:40:49,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:40:49,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:40:49,773] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:40:49,773] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 22:40:49,773] [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
Cocleimonas flava	strain=DSM 24830	GCA_004339015.1	634765	634765	type	True	76.9881	133	666	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:40:49,776] [INFO] DFAST Taxonomy check result was written to GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/tc_result.tsv
[2023-06-12 22:40:49,777] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:40:49,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:40:49,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference/checkm_data
[2023-06-12 22:40:49,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:40:49,818] [INFO] Task started: CheckM
[2023-06-12 22:40:49,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/checkm_input GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/checkm_result
[2023-06-12 22:41:09,814] [INFO] Task succeeded: CheckM
[2023-06-12 22:41:09,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:41:09,837] [INFO] ===== Completeness check finished =====
[2023-06-12 22:41:09,837] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:41:09,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/markers.fasta)
[2023-06-12 22:41:09,838] [INFO] Task started: Blastn
[2023-06-12 22:41:09,838] [INFO] Running command: blastn -query GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f2cba8-1fa5-4010-8c41-4bd64136710c/dqc_reference/reference_markers_gtdb.fasta -out GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:10,580] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:10,586] [INFO] Selected 20 target genomes.
[2023-06-12 22:41:10,586] [INFO] Target genome list was writen to GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:41:10,596] [INFO] Task started: fastANI
[2023-06-12 22:41:10,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg1df2d4ae-24c9-4e04-96ca-d56de7f86a98/GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna.gz --refList GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:41:18,391] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:18,396] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 22:41:18,396] [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_004339015.1	s__Cocleimonas flava	77.1095	126	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Cocleimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 22:41:18,398] [INFO] GTDB search result was written to GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:41:18,399] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:41:18,401] [INFO] DFAST_QC result json was written to GCA_938041705.1_R3_Bin_METABAT_94_sub_1_genomic.fna/dqc_result.json
[2023-06-12 22:41:18,402] [INFO] DFAST_QC completed!
[2023-06-12 22:41:18,402] [INFO] Total running time: 0h0m44s