[2023-03-14 12:13:42,662] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:13:42,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:13:42,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference
[2023-03-14 12:13:44,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:13:44,622] [INFO] Task started: Prodigal
[2023-03-14 12:13:44,622] [INFO] Running command: cat /var/lib/cwl/stgd515034d-90b3-407e-be3a-dd63eba327ab/OceanDNA-b31567.fa | prodigal -d OceanDNA-b31567/cds.fna -a OceanDNA-b31567/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:13:50,259] [INFO] Task succeeded: Prodigal
[2023-03-14 12:13:50,260] [INFO] Task started: HMMsearch
[2023-03-14 12:13:50,260] [INFO] Running command: hmmsearch --tblout OceanDNA-b31567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference/reference_markers.hmm OceanDNA-b31567/protein.faa > /dev/null
[2023-03-14 12:13:50,393] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:13:50,394] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd515034d-90b3-407e-be3a-dd63eba327ab/OceanDNA-b31567.fa]
[2023-03-14 12:13:50,408] [INFO] Query marker FASTA was written to OceanDNA-b31567/markers.fasta
[2023-03-14 12:13:50,410] [INFO] Task started: Blastn
[2023-03-14 12:13:50,410] [INFO] Running command: blastn -query OceanDNA-b31567/markers.fasta -db /var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference/reference_markers.fasta -out OceanDNA-b31567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:13:51,017] [INFO] Task succeeded: Blastn
[2023-03-14 12:13:51,018] [INFO] Selected 7 target genomes.
[2023-03-14 12:13:51,018] [INFO] Target genome list was writen to OceanDNA-b31567/target_genomes.txt
[2023-03-14 12:13:51,023] [INFO] Task started: fastANI
[2023-03-14 12:13:51,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgd515034d-90b3-407e-be3a-dd63eba327ab/OceanDNA-b31567.fa --refList OceanDNA-b31567/target_genomes.txt --output OceanDNA-b31567/fastani_result.tsv --threads 1
[2023-03-14 12:13:54,401] [INFO] Task succeeded: fastANI
[2023-03-14 12:13:54,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:13:54,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:13:54,407] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-03-14 12:13:54,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:13:54,407] [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
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	97.8212	125	137	95	conclusive
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	97.7929	126	137	95	conclusive
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	85.0994	109	137	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	80.9308	94	137	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.8563	95	137	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.2707	57	137	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:13:54,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31567/tc_result.tsv
[2023-03-14 12:13:54,407] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:13:54,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:13:54,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference/checkm_data
[2023-03-14 12:13:54,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:13:54,411] [INFO] Task started: CheckM
[2023-03-14 12:13:54,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31567/checkm_input OceanDNA-b31567/checkm_result
[2023-03-14 12:14:14,612] [INFO] Task succeeded: CheckM
[2023-03-14 12:14:14,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:14:14,614] [INFO] ===== Completeness check finished =====
[2023-03-14 12:14:14,615] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:14:14,615] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31567/markers.fasta)
[2023-03-14 12:14:14,616] [INFO] Task started: Blastn
[2023-03-14 12:14:14,616] [INFO] Running command: blastn -query OceanDNA-b31567/markers.fasta -db /var/lib/cwl/stg0d3f6998-bd71-40d5-8dae-4d437001d648/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:14:15,560] [INFO] Task succeeded: Blastn
[2023-03-14 12:14:15,561] [INFO] Selected 9 target genomes.
[2023-03-14 12:14:15,561] [INFO] Target genome list was writen to OceanDNA-b31567/target_genomes_gtdb.txt
[2023-03-14 12:14:15,574] [INFO] Task started: fastANI
[2023-03-14 12:14:15,574] [INFO] Running command: fastANI --query /var/lib/cwl/stgd515034d-90b3-407e-be3a-dd63eba327ab/OceanDNA-b31567.fa --refList OceanDNA-b31567/target_genomes_gtdb.txt --output OceanDNA-b31567/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:14:19,832] [INFO] Task succeeded: fastANI
[2023-03-14 12:14:19,836] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:14:19,836] [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
GCF_001028625.1	s__Pelagerythrobacter marensis	97.8212	125	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009827515.1	s__Pelagerythrobacter marinus	85.0994	109	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	80.9308	94	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	80.8563	95	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	80.705	95	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.5782	67	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:14:19,837] [INFO] GTDB search result was written to OceanDNA-b31567/result_gtdb.tsv
[2023-03-14 12:14:19,837] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:14:19,838] [INFO] DFAST_QC result json was written to OceanDNA-b31567/dqc_result.json
[2023-03-14 12:14:19,838] [INFO] DFAST_QC completed!
[2023-03-14 12:14:19,838] [INFO] Total running time: 0h0m37s