[2023-06-19 13:14:31,147] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:31,490] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:31,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference
[2023-06-19 13:14:34,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:34,459] [INFO] Task started: Prodigal
[2023-06-19 13:14:34,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c070e64-19d9-40a9-be10-e5e419236e7c/GCA_018668795.1_ASM1866879v1_genomic.fna.gz | prodigal -d GCA_018668795.1_ASM1866879v1_genomic.fna/cds.fna -a GCA_018668795.1_ASM1866879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:40,329] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:40,330] [INFO] Task started: HMMsearch
[2023-06-19 13:14:40,330] [INFO] Running command: hmmsearch --tblout GCA_018668795.1_ASM1866879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference/reference_markers.hmm GCA_018668795.1_ASM1866879v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:40,580] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:40,581] [INFO] Found 6/6 markers.
[2023-06-19 13:14:40,607] [INFO] Query marker FASTA was written to GCA_018668795.1_ASM1866879v1_genomic.fna/markers.fasta
[2023-06-19 13:14:40,608] [INFO] Task started: Blastn
[2023-06-19 13:14:40,608] [INFO] Running command: blastn -query GCA_018668795.1_ASM1866879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference/reference_markers.fasta -out GCA_018668795.1_ASM1866879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:41,271] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:41,275] [INFO] Selected 29 target genomes.
[2023-06-19 13:14:41,276] [INFO] Target genome list was writen to GCA_018668795.1_ASM1866879v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:41,279] [INFO] Task started: fastANI
[2023-06-19 13:14:41,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c070e64-19d9-40a9-be10-e5e419236e7c/GCA_018668795.1_ASM1866879v1_genomic.fna.gz --refList GCA_018668795.1_ASM1866879v1_genomic.fna/target_genomes.txt --output GCA_018668795.1_ASM1866879v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:14:55,892] [INFO] Task succeeded: fastANI
[2023-06-19 13:14:55,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:14:55,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:14:55,895] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:14:55,895] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:14:55,895] [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 13:14:55,897] [INFO] DFAST Taxonomy check result was written to GCA_018668795.1_ASM1866879v1_genomic.fna/tc_result.tsv
[2023-06-19 13:14:55,898] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:14:55,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:14:55,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference/checkm_data
[2023-06-19 13:14:55,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:14:55,937] [INFO] Task started: CheckM
[2023-06-19 13:14:55,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018668795.1_ASM1866879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018668795.1_ASM1866879v1_genomic.fna/checkm_input GCA_018668795.1_ASM1866879v1_genomic.fna/checkm_result
[2023-06-19 13:15:20,808] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:20,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:20,827] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:20,828] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:20,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018668795.1_ASM1866879v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:20,829] [INFO] Task started: Blastn
[2023-06-19 13:15:20,829] [INFO] Running command: blastn -query GCA_018668795.1_ASM1866879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf4d3de-a535-4bf9-b35f-bbe7bdd72d98/dqc_reference/reference_markers_gtdb.fasta -out GCA_018668795.1_ASM1866879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:21,981] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:21,986] [INFO] Selected 16 target genomes.
[2023-06-19 13:15:21,986] [INFO] Target genome list was writen to GCA_018668795.1_ASM1866879v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:21,991] [INFO] Task started: fastANI
[2023-06-19 13:15:21,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c070e64-19d9-40a9-be10-e5e419236e7c/GCA_018668795.1_ASM1866879v1_genomic.fna.gz --refList GCA_018668795.1_ASM1866879v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018668795.1_ASM1866879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:15:27,812] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:27,825] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:15:27,825] [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_018668795.1	s__Puniceispirillum sp018668795	100.0	622	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	99.26	99.26	0.87	0.87	2	conclusive
GCF_000024465.1	s__Puniceispirillum marinum	83.6698	550	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378605.1	s__UBA3439 sp002378605	77.4136	87	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	-
GCA_905182545.1	s__UBA3439 sp905182545	77.2403	107	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.9844	75	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859295.1	s__UBA3439 sp017859295	76.8994	101	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_009919335.1	s__UBA3439 sp009919335	76.7826	64	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_016778895.1	s__UBA3439 sp016778895	76.7257	66	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.63	99.63	0.87	0.87	2	-
GCA_016780525.1	s__UBA3439 sp016780525	76.3705	66	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.22	99.22	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-06-19 13:15:27,827] [INFO] GTDB search result was written to GCA_018668795.1_ASM1866879v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:15:27,828] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:15:27,830] [INFO] DFAST_QC result json was written to GCA_018668795.1_ASM1866879v1_genomic.fna/dqc_result.json
[2023-06-19 13:15:27,830] [INFO] DFAST_QC completed!
[2023-06-19 13:15:27,831] [INFO] Total running time: 0h0m57s