[2023-06-16 22:13:47,318] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:13:47,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:13:47,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference
[2023-06-16 22:13:49,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:13:49,838] [INFO] Task started: Prodigal
[2023-06-16 22:13:49,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg67b5b6a5-f5e1-4af0-8b1d-ad40e5490ff7/GCA_905182005.1_FRAM18_bin263_genomic.fna.gz | prodigal -d GCA_905182005.1_FRAM18_bin263_genomic.fna/cds.fna -a GCA_905182005.1_FRAM18_bin263_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:13:55,496] [INFO] Task succeeded: Prodigal
[2023-06-16 22:13:55,497] [INFO] Task started: HMMsearch
[2023-06-16 22:13:55,497] [INFO] Running command: hmmsearch --tblout GCA_905182005.1_FRAM18_bin263_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference/reference_markers.hmm GCA_905182005.1_FRAM18_bin263_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:13:55,838] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:13:55,839] [INFO] Found 6/6 markers.
[2023-06-16 22:13:55,862] [INFO] Query marker FASTA was written to GCA_905182005.1_FRAM18_bin263_genomic.fna/markers.fasta
[2023-06-16 22:13:55,863] [INFO] Task started: Blastn
[2023-06-16 22:13:55,863] [INFO] Running command: blastn -query GCA_905182005.1_FRAM18_bin263_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference/reference_markers.fasta -out GCA_905182005.1_FRAM18_bin263_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:56,473] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:56,481] [INFO] Selected 30 target genomes.
[2023-06-16 22:13:56,481] [INFO] Target genome list was writen to GCA_905182005.1_FRAM18_bin263_genomic.fna/target_genomes.txt
[2023-06-16 22:13:56,537] [INFO] Task started: fastANI
[2023-06-16 22:13:56,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b5b6a5-f5e1-4af0-8b1d-ad40e5490ff7/GCA_905182005.1_FRAM18_bin263_genomic.fna.gz --refList GCA_905182005.1_FRAM18_bin263_genomic.fna/target_genomes.txt --output GCA_905182005.1_FRAM18_bin263_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:14:18,288] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:18,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:14:18,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:14:18,292] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:14:18,292] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:14:18,292] [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
--------------------------------------------------------------------------------
[2023-06-16 22:14:18,295] [INFO] DFAST Taxonomy check result was written to GCA_905182005.1_FRAM18_bin263_genomic.fna/tc_result.tsv
[2023-06-16 22:14:18,296] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:14:18,296] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:14:18,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference/checkm_data
[2023-06-16 22:14:18,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:14:18,326] [INFO] Task started: CheckM
[2023-06-16 22:14:18,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905182005.1_FRAM18_bin263_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905182005.1_FRAM18_bin263_genomic.fna/checkm_input GCA_905182005.1_FRAM18_bin263_genomic.fna/checkm_result
[2023-06-16 22:14:41,716] [INFO] Task succeeded: CheckM
[2023-06-16 22:14:41,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:14:41,737] [INFO] ===== Completeness check finished =====
[2023-06-16 22:14:41,737] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:14:41,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905182005.1_FRAM18_bin263_genomic.fna/markers.fasta)
[2023-06-16 22:14:41,738] [INFO] Task started: Blastn
[2023-06-16 22:14:41,738] [INFO] Running command: blastn -query GCA_905182005.1_FRAM18_bin263_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ce77df6-1fd6-4fc6-b34e-b792aa7060bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_905182005.1_FRAM18_bin263_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:14:42,525] [INFO] Task succeeded: Blastn
[2023-06-16 22:14:42,528] [INFO] Selected 17 target genomes.
[2023-06-16 22:14:42,529] [INFO] Target genome list was writen to GCA_905182005.1_FRAM18_bin263_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:14:42,557] [INFO] Task started: fastANI
[2023-06-16 22:14:42,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b5b6a5-f5e1-4af0-8b1d-ad40e5490ff7/GCA_905182005.1_FRAM18_bin263_genomic.fna.gz --refList GCA_905182005.1_FRAM18_bin263_genomic.fna/target_genomes_gtdb.txt --output GCA_905182005.1_FRAM18_bin263_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:14:50,394] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:50,408] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:14:50,408] [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_002335115.1	s__ASP10-02a sp002335115	95.3562	592	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.15	95.37	0.85	0.79	13	conclusive
GCA_905182035.1	s__ASP10-02a sp905182035	79.2056	372	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002312935.1	s__ASP10-02a sp002312935	78.4204	319	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.42	99.42	0.91	0.91	2	-
GCA_002470565.1	s__ASP10-02a sp002470565	78.2018	236	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.72	99.72	0.90	0.90	2	-
GCA_003523085.1	s__ASP10-02a sp003523085	77.6629	175	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647765.1	s__ASP10-02a sp018647765	77.6227	182	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.86	99.85	0.95	0.93	3	-
GCA_003521845.1	s__ASP10-02a sp003521845	76.5413	58	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:14:50,411] [INFO] GTDB search result was written to GCA_905182005.1_FRAM18_bin263_genomic.fna/result_gtdb.tsv
[2023-06-16 22:14:50,411] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:14:50,415] [INFO] DFAST_QC result json was written to GCA_905182005.1_FRAM18_bin263_genomic.fna/dqc_result.json
[2023-06-16 22:14:50,415] [INFO] DFAST_QC completed!
[2023-06-16 22:14:50,415] [INFO] Total running time: 0h1m3s