[2023-03-15 07:52:40,323] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,323] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,323] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference
[2023-03-15 07:52:41,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,602] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,602] [INFO] Running command: cat /var/lib/cwl/stg4178deed-70d6-4787-882e-bdbf257fc6c2/OceanDNA-b28818.fa | prodigal -d OceanDNA-b28818/cds.fna -a OceanDNA-b28818/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:46,864] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:46,864] [INFO] Task started: HMMsearch
[2023-03-15 07:52:46,864] [INFO] Running command: hmmsearch --tblout OceanDNA-b28818/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference/reference_markers.hmm OceanDNA-b28818/protein.faa > /dev/null
[2023-03-15 07:52:47,204] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:47,204] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4178deed-70d6-4787-882e-bdbf257fc6c2/OceanDNA-b28818.fa]
[2023-03-15 07:52:47,220] [INFO] Query marker FASTA was written to OceanDNA-b28818/markers.fasta
[2023-03-15 07:52:47,221] [INFO] Task started: Blastn
[2023-03-15 07:52:47,221] [INFO] Running command: blastn -query OceanDNA-b28818/markers.fasta -db /var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference/reference_markers.fasta -out OceanDNA-b28818/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:47,742] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:47,742] [INFO] Selected 14 target genomes.
[2023-03-15 07:52:47,743] [INFO] Target genome list was writen to OceanDNA-b28818/target_genomes.txt
[2023-03-15 07:52:47,751] [INFO] Task started: fastANI
[2023-03-15 07:52:47,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg4178deed-70d6-4787-882e-bdbf257fc6c2/OceanDNA-b28818.fa --refList OceanDNA-b28818/target_genomes.txt --output OceanDNA-b28818/fastani_result.tsv --threads 1
[2023-03-15 07:52:52,835] [INFO] Task succeeded: fastANI
[2023-03-15 07:52:52,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:52:52,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:52:52,836] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:52:52,836] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:52:52,836] [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
--------------------------------------------------------------------------------
[2023-03-15 07:52:52,837] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28818/tc_result.tsv
[2023-03-15 07:52:52,837] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:52:52,837] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:52:52,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference/checkm_data
[2023-03-15 07:52:52,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:52:52,842] [INFO] Task started: CheckM
[2023-03-15 07:52:52,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28818/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28818/checkm_input OceanDNA-b28818/checkm_result
[2023-03-15 07:53:11,866] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:11,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.06%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:11,868] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:11,868] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:11,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28818/markers.fasta)
[2023-03-15 07:53:11,868] [INFO] Task started: Blastn
[2023-03-15 07:53:11,868] [INFO] Running command: blastn -query OceanDNA-b28818/markers.fasta -db /var/lib/cwl/stgeb37da17-0ede-4f1e-95a9-e4933f4945dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28818/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:12,297] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:12,297] [INFO] Selected 11 target genomes.
[2023-03-15 07:53:12,297] [INFO] Target genome list was writen to OceanDNA-b28818/target_genomes_gtdb.txt
[2023-03-15 07:53:12,311] [INFO] Task started: fastANI
[2023-03-15 07:53:12,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg4178deed-70d6-4787-882e-bdbf257fc6c2/OceanDNA-b28818.fa --refList OceanDNA-b28818/target_genomes_gtdb.txt --output OceanDNA-b28818/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:16,221] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:16,226] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:53:16,226] [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_902632125.1	s__MED-G52 sp902632125	95.923	210	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902534325.1	s__MED-G52 sp902534325	82.6759	201	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554705.1	s__MED-G52 sp902554705	82.2682	178	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543185.1	s__MED-G52 sp902543185	81.9183	211	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606585.1	s__MED-G52 sp902606585	81.8078	157	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270125.1	s__MED-G52 sp001627375	77.9409	143	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	97.90	95.50	0.79	0.63	16	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:16,226] [INFO] GTDB search result was written to OceanDNA-b28818/result_gtdb.tsv
[2023-03-15 07:53:16,226] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:16,227] [INFO] DFAST_QC result json was written to OceanDNA-b28818/dqc_result.json
[2023-03-15 07:53:16,227] [INFO] DFAST_QC completed!
[2023-03-15 07:53:16,227] [INFO] Total running time: 0h0m36s