[2023-06-18 12:48:47,973] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:48:47,976] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:48:47,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference
[2023-06-18 12:48:49,695] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:48:49,696] [INFO] Task started: Prodigal
[2023-06-18 12:48:49,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgc895ae0c-0b54-4d56-8c56-8771d41decca/GCA_018607445.1_ASM1860744v1_genomic.fna.gz | prodigal -d GCA_018607445.1_ASM1860744v1_genomic.fna/cds.fna -a GCA_018607445.1_ASM1860744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:48:55,051] [INFO] Task succeeded: Prodigal
[2023-06-18 12:48:55,051] [INFO] Task started: HMMsearch
[2023-06-18 12:48:55,051] [INFO] Running command: hmmsearch --tblout GCA_018607445.1_ASM1860744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference/reference_markers.hmm GCA_018607445.1_ASM1860744v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:48:55,315] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:48:55,317] [INFO] Found 6/6 markers.
[2023-06-18 12:48:55,353] [INFO] Query marker FASTA was written to GCA_018607445.1_ASM1860744v1_genomic.fna/markers.fasta
[2023-06-18 12:48:55,353] [INFO] Task started: Blastn
[2023-06-18 12:48:55,354] [INFO] Running command: blastn -query GCA_018607445.1_ASM1860744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference/reference_markers.fasta -out GCA_018607445.1_ASM1860744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:48:56,095] [INFO] Task succeeded: Blastn
[2023-06-18 12:48:56,103] [INFO] Selected 31 target genomes.
[2023-06-18 12:48:56,104] [INFO] Target genome list was writen to GCA_018607445.1_ASM1860744v1_genomic.fna/target_genomes.txt
[2023-06-18 12:48:56,114] [INFO] Task started: fastANI
[2023-06-18 12:48:56,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgc895ae0c-0b54-4d56-8c56-8771d41decca/GCA_018607445.1_ASM1860744v1_genomic.fna.gz --refList GCA_018607445.1_ASM1860744v1_genomic.fna/target_genomes.txt --output GCA_018607445.1_ASM1860744v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:49:19,871] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:19,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:49:19,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:49:19,875] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:49:19,875] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:49:19,876] [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
--------------------------------------------------------------------------------
[2023-06-18 12:49:19,878] [INFO] DFAST Taxonomy check result was written to GCA_018607445.1_ASM1860744v1_genomic.fna/tc_result.tsv
[2023-06-18 12:49:19,879] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:49:19,879] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:49:19,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference/checkm_data
[2023-06-18 12:49:19,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:49:19,914] [INFO] Task started: CheckM
[2023-06-18 12:49:19,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607445.1_ASM1860744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607445.1_ASM1860744v1_genomic.fna/checkm_input GCA_018607445.1_ASM1860744v1_genomic.fna/checkm_result
[2023-06-18 12:49:42,453] [INFO] Task succeeded: CheckM
[2023-06-18 12:49:42,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:49:42,482] [INFO] ===== Completeness check finished =====
[2023-06-18 12:49:42,483] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:49:42,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607445.1_ASM1860744v1_genomic.fna/markers.fasta)
[2023-06-18 12:49:42,483] [INFO] Task started: Blastn
[2023-06-18 12:49:42,484] [INFO] Running command: blastn -query GCA_018607445.1_ASM1860744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6453d2ee-0fd6-46f0-b8d2-20b7668072c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607445.1_ASM1860744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:49:43,643] [INFO] Task succeeded: Blastn
[2023-06-18 12:49:43,651] [INFO] Selected 14 target genomes.
[2023-06-18 12:49:43,651] [INFO] Target genome list was writen to GCA_018607445.1_ASM1860744v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:49:43,656] [INFO] Task started: fastANI
[2023-06-18 12:49:43,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgc895ae0c-0b54-4d56-8c56-8771d41decca/GCA_018607445.1_ASM1860744v1_genomic.fna.gz --refList GCA_018607445.1_ASM1860744v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607445.1_ASM1860744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:49:50,839] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:50,853] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:49:50,853] [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_002334915.1	s__HTCC2207 sp002334915	99.5242	546	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	conclusive
GCA_002378645.1	s__HTCC2207 sp002378645	83.8786	493	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_018664075.1	s__HTCC2207 sp018664075	80.7807	315	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.4145	324	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663035.1	s__HTCC2207 sp018663035	78.1706	234	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_002335945.1	s__HTCC2207 sp002335945	77.6663	212	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.2337	115	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_002685715.1	s__HTCC2207 sp002685715	77.176	139	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.7127	50	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182855.1	s__HTCC2207 sp905182855	76.6122	80	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:49:50,855] [INFO] GTDB search result was written to GCA_018607445.1_ASM1860744v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:49:50,855] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:49:50,860] [INFO] DFAST_QC result json was written to GCA_018607445.1_ASM1860744v1_genomic.fna/dqc_result.json
[2023-06-18 12:49:50,860] [INFO] DFAST_QC completed!
[2023-06-18 12:49:50,860] [INFO] Total running time: 0h1m3s