[2023-03-18 05:05:08,024] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:05:08,025] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:05:08,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference
[2023-03-18 05:05:09,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:05:09,150] [INFO] Task started: Prodigal
[2023-03-18 05:05:09,150] [INFO] Running command: cat /var/lib/cwl/stg036970d0-17eb-4ba1-9801-db49afdbf704/OceanDNA-b26427.fa | prodigal -d OceanDNA-b26427/cds.fna -a OceanDNA-b26427/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:05:14,522] [INFO] Task succeeded: Prodigal
[2023-03-18 05:05:14,522] [INFO] Task started: HMMsearch
[2023-03-18 05:05:14,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b26427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference/reference_markers.hmm OceanDNA-b26427/protein.faa > /dev/null
[2023-03-18 05:05:14,667] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:05:14,667] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg036970d0-17eb-4ba1-9801-db49afdbf704/OceanDNA-b26427.fa]
[2023-03-18 05:05:14,698] [INFO] Query marker FASTA was written to OceanDNA-b26427/markers.fasta
[2023-03-18 05:05:14,699] [INFO] Task started: Blastn
[2023-03-18 05:05:14,699] [INFO] Running command: blastn -query OceanDNA-b26427/markers.fasta -db /var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference/reference_markers.fasta -out OceanDNA-b26427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:15,252] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:15,256] [INFO] Selected 24 target genomes.
[2023-03-18 05:05:15,257] [INFO] Target genome list was writen to OceanDNA-b26427/target_genomes.txt
[2023-03-18 05:05:15,305] [INFO] Task started: fastANI
[2023-03-18 05:05:15,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg036970d0-17eb-4ba1-9801-db49afdbf704/OceanDNA-b26427.fa --refList OceanDNA-b26427/target_genomes.txt --output OceanDNA-b26427/fastani_result.tsv --threads 1
[2023-03-18 05:05:32,585] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:32,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:05:32,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:05:32,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:05:32,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:05:32,586] [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
--------------------------------------------------------------------------------
[2023-03-18 05:05:32,587] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26427/tc_result.tsv
[2023-03-18 05:05:32,588] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:05:32,589] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:05:32,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference/checkm_data
[2023-03-18 05:05:32,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:05:32,596] [INFO] Task started: CheckM
[2023-03-18 05:05:32,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26427/checkm_input OceanDNA-b26427/checkm_result
[2023-03-18 05:05:52,336] [INFO] Task succeeded: CheckM
[2023-03-18 05:05:52,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.37%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:05:52,356] [INFO] ===== Completeness check finished =====
[2023-03-18 05:05:52,356] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:05:52,356] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26427/markers.fasta)
[2023-03-18 05:05:52,356] [INFO] Task started: Blastn
[2023-03-18 05:05:52,357] [INFO] Running command: blastn -query OceanDNA-b26427/markers.fasta -db /var/lib/cwl/stg196bf33b-7dd7-4ec2-9a58-a56d2a55c52f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:53,229] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:53,231] [INFO] Selected 12 target genomes.
[2023-03-18 05:05:53,231] [INFO] Target genome list was writen to OceanDNA-b26427/target_genomes_gtdb.txt
[2023-03-18 05:05:53,376] [INFO] Task started: fastANI
[2023-03-18 05:05:53,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg036970d0-17eb-4ba1-9801-db49afdbf704/OceanDNA-b26427.fa --refList OceanDNA-b26427/target_genomes_gtdb.txt --output OceanDNA-b26427/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:05:57,080] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:57,086] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:05:57,086] [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_004213025.1	s__UBA8309 sp004213025	88.4839	117	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	84.3055	178	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	84.1403	175	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	79.6827	124	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	79.118	97	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780765.1	s__UBA8309 sp016780765	78.1027	67	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002686685.1	s__UBA8309 sp002686685	78.0289	60	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_002683535.1	s__UBA8309 sp002683535	77.273	52	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524735.1	s__UBA8309 sp011524735	77.2158	53	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:05:57,088] [INFO] GTDB search result was written to OceanDNA-b26427/result_gtdb.tsv
[2023-03-18 05:05:57,090] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:05:57,092] [INFO] DFAST_QC result json was written to OceanDNA-b26427/dqc_result.json
[2023-03-18 05:05:57,092] [INFO] DFAST_QC completed!
[2023-03-18 05:05:57,092] [INFO] Total running time: 0h0m49s