[2023-03-18 08:17:17,677] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,678] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference
[2023-03-18 08:17:18,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,944] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,944] [INFO] Running command: cat /var/lib/cwl/stgb879cf5c-8dcd-4d4d-b007-de7bb80c9a34/OceanDNA-b23459.fa | prodigal -d OceanDNA-b23459/cds.fna -a OceanDNA-b23459/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:24,779] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:24,780] [INFO] Task started: HMMsearch
[2023-03-18 08:17:24,780] [INFO] Running command: hmmsearch --tblout OceanDNA-b23459/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference/reference_markers.hmm OceanDNA-b23459/protein.faa > /dev/null
[2023-03-18 08:17:24,959] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:24,959] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb879cf5c-8dcd-4d4d-b007-de7bb80c9a34/OceanDNA-b23459.fa]
[2023-03-18 08:17:24,976] [INFO] Query marker FASTA was written to OceanDNA-b23459/markers.fasta
[2023-03-18 08:17:24,976] [INFO] Task started: Blastn
[2023-03-18 08:17:24,976] [INFO] Running command: blastn -query OceanDNA-b23459/markers.fasta -db /var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference/reference_markers.fasta -out OceanDNA-b23459/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:25,576] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:25,577] [INFO] Selected 15 target genomes.
[2023-03-18 08:17:25,577] [INFO] Target genome list was writen to OceanDNA-b23459/target_genomes.txt
[2023-03-18 08:17:25,585] [INFO] Task started: fastANI
[2023-03-18 08:17:25,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgb879cf5c-8dcd-4d4d-b007-de7bb80c9a34/OceanDNA-b23459.fa --refList OceanDNA-b23459/target_genomes.txt --output OceanDNA-b23459/fastani_result.tsv --threads 1
[2023-03-18 08:17:34,624] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:34,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:34,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:34,629] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:34,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:34,630] [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
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	81.5353	55	90	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	80.4529	51	90	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.0129	57	90	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.8873	50	90	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.7514	58	90	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:34,630] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23459/tc_result.tsv
[2023-03-18 08:17:34,630] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:34,630] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:34,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference/checkm_data
[2023-03-18 08:17:34,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:34,635] [INFO] Task started: CheckM
[2023-03-18 08:17:34,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23459/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23459/checkm_input OceanDNA-b23459/checkm_result
[2023-03-18 08:17:55,188] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:55,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.11%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:17:55,190] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:55,191] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:55,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23459/markers.fasta)
[2023-03-18 08:17:55,191] [INFO] Task started: Blastn
[2023-03-18 08:17:55,191] [INFO] Running command: blastn -query OceanDNA-b23459/markers.fasta -db /var/lib/cwl/stgbd2d89b7-5e97-469d-a702-56e89eea424d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23459/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:56,058] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:56,059] [INFO] Selected 13 target genomes.
[2023-03-18 08:17:56,059] [INFO] Target genome list was writen to OceanDNA-b23459/target_genomes_gtdb.txt
[2023-03-18 08:17:56,105] [INFO] Task started: fastANI
[2023-03-18 08:17:56,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgb879cf5c-8dcd-4d4d-b007-de7bb80c9a34/OceanDNA-b23459.fa --refList OceanDNA-b23459/target_genomes_gtdb.txt --output OceanDNA-b23459/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:04,096] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:04,102] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:18:04,102] [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_013911965.1	s__Phenylobacterium sp013911965	98.0051	85	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	conclusive
GCA_002363865.1	s__Phenylobacterium sp002363865	82.4705	70	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCF_000017265.1	s__Phenylobacterium zucineum	81.5353	55	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_002441055.1	s__Phenylobacterium sp002441055	81.2517	60	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196295.1	s__Phenylobacterium haematophilum	79.8873	50	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	79.706	53	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	79.2627	54	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136395.1	s__Phenylobacterium sp003136395	79.224	50	90	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:04,103] [INFO] GTDB search result was written to OceanDNA-b23459/result_gtdb.tsv
[2023-03-18 08:18:04,103] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:04,104] [INFO] DFAST_QC result json was written to OceanDNA-b23459/dqc_result.json
[2023-03-18 08:18:04,104] [INFO] DFAST_QC completed!
[2023-03-18 08:18:04,104] [INFO] Total running time: 0h0m46s