[2023-03-16 09:49:19,907] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:49:19,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:49:19,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference
[2023-03-16 09:49:20,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:49:20,972] [INFO] Task started: Prodigal
[2023-03-16 09:49:20,972] [INFO] Running command: cat /var/lib/cwl/stg8b7357f6-e4df-4611-87c5-f0eca0b84b59/OceanDNA-b32484.fa | prodigal -d OceanDNA-b32484/cds.fna -a OceanDNA-b32484/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:49:25,782] [INFO] Task succeeded: Prodigal
[2023-03-16 09:49:25,783] [INFO] Task started: HMMsearch
[2023-03-16 09:49:25,783] [INFO] Running command: hmmsearch --tblout OceanDNA-b32484/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference/reference_markers.hmm OceanDNA-b32484/protein.faa > /dev/null
[2023-03-16 09:49:25,934] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:49:25,935] [INFO] Found 6/6 markers.
[2023-03-16 09:49:25,951] [INFO] Query marker FASTA was written to OceanDNA-b32484/markers.fasta
[2023-03-16 09:49:25,951] [INFO] Task started: Blastn
[2023-03-16 09:49:25,951] [INFO] Running command: blastn -query OceanDNA-b32484/markers.fasta -db /var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference/reference_markers.fasta -out OceanDNA-b32484/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:49:26,466] [INFO] Task succeeded: Blastn
[2023-03-16 09:49:26,468] [INFO] Selected 12 target genomes.
[2023-03-16 09:49:26,468] [INFO] Target genome list was writen to OceanDNA-b32484/target_genomes.txt
[2023-03-16 09:49:26,477] [INFO] Task started: fastANI
[2023-03-16 09:49:26,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7357f6-e4df-4611-87c5-f0eca0b84b59/OceanDNA-b32484.fa --refList OceanDNA-b32484/target_genomes.txt --output OceanDNA-b32484/fastani_result.tsv --threads 1
[2023-03-16 09:49:32,594] [INFO] Task succeeded: fastANI
[2023-03-16 09:49:32,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:49:32,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:49:32,595] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:49:32,595] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:49:32,595] [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
--------------------------------------------------------------------------------
[2023-03-16 09:49:32,596] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32484/tc_result.tsv
[2023-03-16 09:49:32,598] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:49:32,598] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:49:32,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference/checkm_data
[2023-03-16 09:49:32,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:49:32,605] [INFO] Task started: CheckM
[2023-03-16 09:49:32,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32484/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32484/checkm_input OceanDNA-b32484/checkm_result
[2023-03-16 09:49:51,240] [INFO] Task succeeded: CheckM
[2023-03-16 09:49:51,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.66%
Contamintation: 9.70%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:49:51,323] [INFO] ===== Completeness check finished =====
[2023-03-16 09:49:51,323] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:49:51,323] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32484/markers.fasta)
[2023-03-16 09:49:51,324] [INFO] Task started: Blastn
[2023-03-16 09:49:51,324] [INFO] Running command: blastn -query OceanDNA-b32484/markers.fasta -db /var/lib/cwl/stg8a43aa5d-832c-45d0-98ad-0c53911fc731/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32484/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:49:52,072] [INFO] Task succeeded: Blastn
[2023-03-16 09:49:52,074] [INFO] Selected 15 target genomes.
[2023-03-16 09:49:52,075] [INFO] Target genome list was writen to OceanDNA-b32484/target_genomes_gtdb.txt
[2023-03-16 09:49:52,084] [INFO] Task started: fastANI
[2023-03-16 09:49:52,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7357f6-e4df-4611-87c5-f0eca0b84b59/OceanDNA-b32484.fa --refList OceanDNA-b32484/target_genomes_gtdb.txt --output OceanDNA-b32484/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:49:55,226] [INFO] Task succeeded: fastANI
[2023-03-16 09:49:55,231] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:49:55,231] [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_902615805.1	s__TMED62 sp902615805	83.7027	166	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902527765.1	s__TMED62 sp902527765	83.2708	114	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547175.1	s__TMED62 sp902547175	83.2004	114	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614225.1	s__TMED62 sp902614225	83.1358	128	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571315.1	s__TMED62 sp902571315	82.0739	130	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170595.1	s__TMED62 sp002170595	78.7878	156	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	99.91	99.91	0.92	0.92	2	-
GCA_002715505.1	s__GCA-2715505 sp002715505	76.3089	56	272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2715505	95.0	99.85	99.85	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:49:55,233] [INFO] GTDB search result was written to OceanDNA-b32484/result_gtdb.tsv
[2023-03-16 09:49:55,233] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:49:55,234] [INFO] DFAST_QC result json was written to OceanDNA-b32484/dqc_result.json
[2023-03-16 09:49:55,235] [INFO] DFAST_QC completed!
[2023-03-16 09:49:55,235] [INFO] Total running time: 0h0m35s