[2023-06-19 01:24:11,898] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:24:11,903] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:24:11,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference
[2023-06-19 01:24:15,311] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:24:15,312] [INFO] Task started: Prodigal
[2023-06-19 01:24:15,312] [INFO] Running command: gunzip -c /var/lib/cwl/stga50e94e2-7513-4a3d-9f5d-3dde38687a05/GCA_018055945.1_ASM1805594v1_genomic.fna.gz | prodigal -d GCA_018055945.1_ASM1805594v1_genomic.fna/cds.fna -a GCA_018055945.1_ASM1805594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:24:23,769] [INFO] Task succeeded: Prodigal
[2023-06-19 01:24:23,769] [INFO] Task started: HMMsearch
[2023-06-19 01:24:23,769] [INFO] Running command: hmmsearch --tblout GCA_018055945.1_ASM1805594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference/reference_markers.hmm GCA_018055945.1_ASM1805594v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:24:24,082] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:24:24,086] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga50e94e2-7513-4a3d-9f5d-3dde38687a05/GCA_018055945.1_ASM1805594v1_genomic.fna.gz]
[2023-06-19 01:24:24,119] [INFO] Query marker FASTA was written to GCA_018055945.1_ASM1805594v1_genomic.fna/markers.fasta
[2023-06-19 01:24:24,120] [INFO] Task started: Blastn
[2023-06-19 01:24:24,120] [INFO] Running command: blastn -query GCA_018055945.1_ASM1805594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference/reference_markers.fasta -out GCA_018055945.1_ASM1805594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:24:24,989] [INFO] Task succeeded: Blastn
[2023-06-19 01:24:24,995] [INFO] Selected 25 target genomes.
[2023-06-19 01:24:24,995] [INFO] Target genome list was writen to GCA_018055945.1_ASM1805594v1_genomic.fna/target_genomes.txt
[2023-06-19 01:24:24,998] [INFO] Task started: fastANI
[2023-06-19 01:24:24,999] [INFO] Running command: fastANI --query /var/lib/cwl/stga50e94e2-7513-4a3d-9f5d-3dde38687a05/GCA_018055945.1_ASM1805594v1_genomic.fna.gz --refList GCA_018055945.1_ASM1805594v1_genomic.fna/target_genomes.txt --output GCA_018055945.1_ASM1805594v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:24:43,652] [INFO] Task succeeded: fastANI
[2023-06-19 01:24:43,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:24:43,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:24:43,674] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:24:43,674] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:24:43,674] [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
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	76.3278	50	805	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.071	58	805	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.9372	82	805	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	75.9259	53	805	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.6048	83	805	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:24:43,677] [INFO] DFAST Taxonomy check result was written to GCA_018055945.1_ASM1805594v1_genomic.fna/tc_result.tsv
[2023-06-19 01:24:43,677] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:24:43,678] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:24:43,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference/checkm_data
[2023-06-19 01:24:43,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:24:43,727] [INFO] Task started: CheckM
[2023-06-19 01:24:43,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018055945.1_ASM1805594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018055945.1_ASM1805594v1_genomic.fna/checkm_input GCA_018055945.1_ASM1805594v1_genomic.fna/checkm_result
[2023-06-19 01:25:13,653] [INFO] Task succeeded: CheckM
[2023-06-19 01:25:13,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:25:13,687] [INFO] ===== Completeness check finished =====
[2023-06-19 01:25:13,687] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:25:13,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018055945.1_ASM1805594v1_genomic.fna/markers.fasta)
[2023-06-19 01:25:13,688] [INFO] Task started: Blastn
[2023-06-19 01:25:13,688] [INFO] Running command: blastn -query GCA_018055945.1_ASM1805594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06433465-742c-42ff-8f5a-687b80eb9b1d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018055945.1_ASM1805594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:25:14,991] [INFO] Task succeeded: Blastn
[2023-06-19 01:25:14,999] [INFO] Selected 13 target genomes.
[2023-06-19 01:25:14,999] [INFO] Target genome list was writen to GCA_018055945.1_ASM1805594v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:25:15,003] [INFO] Task started: fastANI
[2023-06-19 01:25:15,004] [INFO] Running command: fastANI --query /var/lib/cwl/stga50e94e2-7513-4a3d-9f5d-3dde38687a05/GCA_018055945.1_ASM1805594v1_genomic.fna.gz --refList GCA_018055945.1_ASM1805594v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018055945.1_ASM1805594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:25:22,551] [INFO] Task succeeded: fastANI
[2023-06-19 01:25:22,563] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 01:25:22,563] [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_016705365.1	s__UBA5518 sp002396625	85.5348	689	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	99.76	99.45	0.96	0.89	14	-
GCA_016718385.1	s__UBA5518 sp016718385	78.3256	341	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	98.99	98.50	0.94	0.92	5	-
GCA_018057015.1	s__UBA5518 sp018057015	77.9427	237	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928015.1	s__UBA5518 sp903928015	76.9846	136	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	99.79	99.63	0.93	0.92	4	-
GCA_903938575.1	s__UBA5518 sp903938575	76.7427	146	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	98.92	98.84	0.83	0.82	4	-
GCA_903921135.1	s__UBA5518 sp903921135	76.5639	132	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	97.78	97.78	0.78	0.78	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	75.9526	65	805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:25:22,566] [INFO] GTDB search result was written to GCA_018055945.1_ASM1805594v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:25:22,566] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:25:22,571] [INFO] DFAST_QC result json was written to GCA_018055945.1_ASM1805594v1_genomic.fna/dqc_result.json
[2023-06-19 01:25:22,571] [INFO] DFAST_QC completed!
[2023-06-19 01:25:22,571] [INFO] Total running time: 0h1m11s