[2023-03-15 11:20:29,257] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference
[2023-03-15 11:20:30,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,350] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,350] [INFO] Running command: cat /var/lib/cwl/stg00334ecd-7005-4b7f-b7d1-5f3163971eac/OceanDNA-b38359.fa | prodigal -d OceanDNA-b38359/cds.fna -a OceanDNA-b38359/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:43,797] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:43,797] [INFO] Task started: HMMsearch
[2023-03-15 11:20:43,797] [INFO] Running command: hmmsearch --tblout OceanDNA-b38359/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference/reference_markers.hmm OceanDNA-b38359/protein.faa > /dev/null
[2023-03-15 11:20:44,015] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:44,015] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00334ecd-7005-4b7f-b7d1-5f3163971eac/OceanDNA-b38359.fa]
[2023-03-15 11:20:44,055] [INFO] Query marker FASTA was written to OceanDNA-b38359/markers.fasta
[2023-03-15 11:20:44,055] [INFO] Task started: Blastn
[2023-03-15 11:20:44,055] [INFO] Running command: blastn -query OceanDNA-b38359/markers.fasta -db /var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference/reference_markers.fasta -out OceanDNA-b38359/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:44,637] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:44,642] [INFO] Selected 36 target genomes.
[2023-03-15 11:20:44,643] [INFO] Target genome list was writen to OceanDNA-b38359/target_genomes.txt
[2023-03-15 11:20:44,667] [INFO] Task started: fastANI
[2023-03-15 11:20:44,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg00334ecd-7005-4b7f-b7d1-5f3163971eac/OceanDNA-b38359.fa --refList OceanDNA-b38359/target_genomes.txt --output OceanDNA-b38359/fastani_result.tsv --threads 1
[2023-03-15 11:21:09,629] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:09,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:21:09,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:21:09,632] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:21:09,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:21:09,632] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	77.3927	143	651	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:21:09,636] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38359/tc_result.tsv
[2023-03-15 11:21:09,640] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:21:09,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:21:09,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference/checkm_data
[2023-03-15 11:21:09,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:21:09,647] [INFO] Task started: CheckM
[2023-03-15 11:21:09,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38359/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38359/checkm_input OceanDNA-b38359/checkm_result
[2023-03-15 11:21:47,872] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:47,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:47,966] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:47,966] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:47,967] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38359/markers.fasta)
[2023-03-15 11:21:47,968] [INFO] Task started: Blastn
[2023-03-15 11:21:47,968] [INFO] Running command: blastn -query OceanDNA-b38359/markers.fasta -db /var/lib/cwl/stg451bfa29-a058-4ce5-9875-32ee01653194/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38359/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:48,851] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:48,855] [INFO] Selected 25 target genomes.
[2023-03-15 11:21:48,855] [INFO] Target genome list was writen to OceanDNA-b38359/target_genomes_gtdb.txt
[2023-03-15 11:21:48,878] [INFO] Task started: fastANI
[2023-03-15 11:21:48,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg00334ecd-7005-4b7f-b7d1-5f3163971eac/OceanDNA-b38359.fa --refList OceanDNA-b38359/target_genomes_gtdb.txt --output OceanDNA-b38359/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:22:05,587] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:05,591] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:22:05,592] [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_002708905.1	s__Ketobacter sp002708905	77.7073	147	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002863865.1	s__Ketobacter alkanivorans	77.3927	143	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	77.3468	152	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
GCA_003671495.1	s__Ketobacter sp003671495	77.2624	155	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701845.1	s__Ketobacter sp002701845	77.218	95	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746715.1	s__Ketobacter sp003667185	76.8817	98	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.27	99.27	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:22:05,593] [INFO] GTDB search result was written to OceanDNA-b38359/result_gtdb.tsv
[2023-03-15 11:22:05,598] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:22:05,603] [INFO] DFAST_QC result json was written to OceanDNA-b38359/dqc_result.json
[2023-03-15 11:22:05,604] [INFO] DFAST_QC completed!
[2023-03-15 11:22:05,604] [INFO] Total running time: 0h1m36s