[2023-06-19 04:14:07,848] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:07,863] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:07,863] [INFO] DQC Reference Directory: /var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference
[2023-06-19 04:14:10,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:10,192] [INFO] Task started: Prodigal
[2023-06-19 04:14:10,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg266eee7c-eac6-4101-8dd4-90b8fecf7795/GCA_018607285.1_ASM1860728v1_genomic.fna.gz | prodigal -d GCA_018607285.1_ASM1860728v1_genomic.fna/cds.fna -a GCA_018607285.1_ASM1860728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:12,955] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:12,956] [INFO] Task started: HMMsearch
[2023-06-19 04:14:12,956] [INFO] Running command: hmmsearch --tblout GCA_018607285.1_ASM1860728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference/reference_markers.hmm GCA_018607285.1_ASM1860728v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:13,202] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:13,204] [INFO] Found 6/6 markers.
[2023-06-19 04:14:13,231] [INFO] Query marker FASTA was written to GCA_018607285.1_ASM1860728v1_genomic.fna/markers.fasta
[2023-06-19 04:14:13,232] [INFO] Task started: Blastn
[2023-06-19 04:14:13,232] [INFO] Running command: blastn -query GCA_018607285.1_ASM1860728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference/reference_markers.fasta -out GCA_018607285.1_ASM1860728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:13,864] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:13,868] [INFO] Selected 15 target genomes.
[2023-06-19 04:14:13,868] [INFO] Target genome list was writen to GCA_018607285.1_ASM1860728v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:13,871] [INFO] Task started: fastANI
[2023-06-19 04:14:13,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg266eee7c-eac6-4101-8dd4-90b8fecf7795/GCA_018607285.1_ASM1860728v1_genomic.fna.gz --refList GCA_018607285.1_ASM1860728v1_genomic.fna/target_genomes.txt --output GCA_018607285.1_ASM1860728v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:14:23,038] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:23,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:14:23,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:14:23,040] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:14:23,040] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:14:23,040] [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
--------------------------------------------------------------------------------
[2023-06-19 04:14:23,042] [INFO] DFAST Taxonomy check result was written to GCA_018607285.1_ASM1860728v1_genomic.fna/tc_result.tsv
[2023-06-19 04:14:23,043] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:14:23,043] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:14:23,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference/checkm_data
[2023-06-19 04:14:23,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:14:23,072] [INFO] Task started: CheckM
[2023-06-19 04:14:23,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607285.1_ASM1860728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607285.1_ASM1860728v1_genomic.fna/checkm_input GCA_018607285.1_ASM1860728v1_genomic.fna/checkm_result
[2023-06-19 04:14:39,830] [INFO] Task succeeded: CheckM
[2023-06-19 04:14:39,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:14:39,853] [INFO] ===== Completeness check finished =====
[2023-06-19 04:14:39,854] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:14:39,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607285.1_ASM1860728v1_genomic.fna/markers.fasta)
[2023-06-19 04:14:39,855] [INFO] Task started: Blastn
[2023-06-19 04:14:39,855] [INFO] Running command: blastn -query GCA_018607285.1_ASM1860728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedabfb26-d198-4d14-b2b5-b4ec865fd30b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607285.1_ASM1860728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:40,830] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:40,835] [INFO] Selected 16 target genomes.
[2023-06-19 04:14:40,835] [INFO] Target genome list was writen to GCA_018607285.1_ASM1860728v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:14:40,843] [INFO] Task started: fastANI
[2023-06-19 04:14:40,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg266eee7c-eac6-4101-8dd4-90b8fecf7795/GCA_018607285.1_ASM1860728v1_genomic.fna.gz --refList GCA_018607285.1_ASM1860728v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607285.1_ASM1860728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:14:45,163] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:45,182] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:14:45,183] [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_002469975.1	s__D2472 sp002469975	99.3813	336	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	conclusive
GCA_002358345.1	s__D2472 sp002358345	82.0636	305	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	-
GCA_905181595.1	s__D2472 sp905181595	80.6414	232	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307935.1	s__D2472 sp000307935	77.9177	104	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596165.1	s__D2472 sp902596165	77.6507	109	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283765.1	s__D2472 sp003283765	77.5928	100	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003284215.1	s__D2472 sp003284215	77.5912	91	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_902515455.1	s__D2472 sp902515455	77.3314	73	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	77.2982	117	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	77.0467	79	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902541245.1	s__D2472 sp902541245	76.8656	55	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515775.1	s__D2472 sp902515775	76.7477	80	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:14:45,185] [INFO] GTDB search result was written to GCA_018607285.1_ASM1860728v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:14:45,185] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:14:45,189] [INFO] DFAST_QC result json was written to GCA_018607285.1_ASM1860728v1_genomic.fna/dqc_result.json
[2023-06-19 04:14:45,189] [INFO] DFAST_QC completed!
[2023-06-19 04:14:45,189] [INFO] Total running time: 0h0m37s