[2023-06-17 11:26:04,764] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:04,767] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:04,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference
[2023-06-17 11:26:06,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:06,635] [INFO] Task started: Prodigal
[2023-06-17 11:26:06,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg85ccf1b1-23a6-4daf-90d0-ef7ec830544c/GCA_905182155.1_FRAM18_bin287_genomic.fna.gz | prodigal -d GCA_905182155.1_FRAM18_bin287_genomic.fna/cds.fna -a GCA_905182155.1_FRAM18_bin287_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:13,105] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:13,106] [INFO] Task started: HMMsearch
[2023-06-17 11:26:13,106] [INFO] Running command: hmmsearch --tblout GCA_905182155.1_FRAM18_bin287_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference/reference_markers.hmm GCA_905182155.1_FRAM18_bin287_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:26:13,397] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:26:13,399] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg85ccf1b1-23a6-4daf-90d0-ef7ec830544c/GCA_905182155.1_FRAM18_bin287_genomic.fna.gz]
[2023-06-17 11:26:13,429] [INFO] Query marker FASTA was written to GCA_905182155.1_FRAM18_bin287_genomic.fna/markers.fasta
[2023-06-17 11:26:13,429] [INFO] Task started: Blastn
[2023-06-17 11:26:13,429] [INFO] Running command: blastn -query GCA_905182155.1_FRAM18_bin287_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference/reference_markers.fasta -out GCA_905182155.1_FRAM18_bin287_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:14,107] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:14,114] [INFO] Selected 20 target genomes.
[2023-06-17 11:26:14,115] [INFO] Target genome list was writen to GCA_905182155.1_FRAM18_bin287_genomic.fna/target_genomes.txt
[2023-06-17 11:26:14,121] [INFO] Task started: fastANI
[2023-06-17 11:26:14,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg85ccf1b1-23a6-4daf-90d0-ef7ec830544c/GCA_905182155.1_FRAM18_bin287_genomic.fna.gz --refList GCA_905182155.1_FRAM18_bin287_genomic.fna/target_genomes.txt --output GCA_905182155.1_FRAM18_bin287_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:26:26,542] [INFO] Task succeeded: fastANI
[2023-06-17 11:26:26,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:26:26,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:26:26,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:26:26,545] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:26:26,545] [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
--------------------------------------------------------------------------------
[2023-06-17 11:26:26,547] [INFO] DFAST Taxonomy check result was written to GCA_905182155.1_FRAM18_bin287_genomic.fna/tc_result.tsv
[2023-06-17 11:26:26,548] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:26:26,548] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:26:26,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference/checkm_data
[2023-06-17 11:26:26,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:26:26,580] [INFO] Task started: CheckM
[2023-06-17 11:26:26,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905182155.1_FRAM18_bin287_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905182155.1_FRAM18_bin287_genomic.fna/checkm_input GCA_905182155.1_FRAM18_bin287_genomic.fna/checkm_result
[2023-06-17 11:26:52,009] [INFO] Task succeeded: CheckM
[2023-06-17 11:26:52,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:26:52,030] [INFO] ===== Completeness check finished =====
[2023-06-17 11:26:52,030] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:26:52,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905182155.1_FRAM18_bin287_genomic.fna/markers.fasta)
[2023-06-17 11:26:52,031] [INFO] Task started: Blastn
[2023-06-17 11:26:52,031] [INFO] Running command: blastn -query GCA_905182155.1_FRAM18_bin287_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e69a6d5-7d7d-41e0-a6fa-d34d3d13f9cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_905182155.1_FRAM18_bin287_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:52,808] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:52,813] [INFO] Selected 14 target genomes.
[2023-06-17 11:26:52,813] [INFO] Target genome list was writen to GCA_905182155.1_FRAM18_bin287_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:26:52,833] [INFO] Task started: fastANI
[2023-06-17 11:26:52,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg85ccf1b1-23a6-4daf-90d0-ef7ec830544c/GCA_905182155.1_FRAM18_bin287_genomic.fna.gz --refList GCA_905182155.1_FRAM18_bin287_genomic.fna/target_genomes_gtdb.txt --output GCA_905182155.1_FRAM18_bin287_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:26:59,877] [INFO] Task succeeded: fastANI
[2023-06-17 11:26:59,883] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:26:59,884] [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_905182155.1	s__UBA9926 sp905182155	99.9995	736	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905182025.1	s__UBA4582 sp905182025	82.9273	66	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854255.1	s__UBA9926 sp003451575	81.1578	498	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.03	98.40	0.91	0.88	11	-
GCA_018645765.1	s__UBA9926 sp018645765	80.2822	283	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647445.1	s__UBA9926 sp018647445	79.7878	393	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-17 11:26:59,886] [INFO] GTDB search result was written to GCA_905182155.1_FRAM18_bin287_genomic.fna/result_gtdb.tsv
[2023-06-17 11:26:59,887] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:26:59,889] [INFO] DFAST_QC result json was written to GCA_905182155.1_FRAM18_bin287_genomic.fna/dqc_result.json
[2023-06-17 11:26:59,889] [INFO] DFAST_QC completed!
[2023-06-17 11:26:59,889] [INFO] Total running time: 0h0m55s