[2023-03-15 22:06:34,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:06:34,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:06:34,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference
[2023-03-15 22:06:35,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:06:35,885] [INFO] Task started: Prodigal
[2023-03-15 22:06:35,885] [INFO] Running command: cat /var/lib/cwl/stg38dc7b6e-8bf3-4045-b330-a09cc687f7d3/OceanDNA-b12609.fa | prodigal -d OceanDNA-b12609/cds.fna -a OceanDNA-b12609/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:06:50,381] [INFO] Task succeeded: Prodigal
[2023-03-15 22:06:50,381] [INFO] Task started: HMMsearch
[2023-03-15 22:06:50,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b12609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference/reference_markers.hmm OceanDNA-b12609/protein.faa > /dev/null
[2023-03-15 22:06:50,560] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:06:50,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg38dc7b6e-8bf3-4045-b330-a09cc687f7d3/OceanDNA-b12609.fa]
[2023-03-15 22:06:50,580] [INFO] Query marker FASTA was written to OceanDNA-b12609/markers.fasta
[2023-03-15 22:06:50,580] [INFO] Task started: Blastn
[2023-03-15 22:06:50,580] [INFO] Running command: blastn -query OceanDNA-b12609/markers.fasta -db /var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference/reference_markers.fasta -out OceanDNA-b12609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:06:51,082] [INFO] Task succeeded: Blastn
[2023-03-15 22:06:51,083] [INFO] Selected 21 target genomes.
[2023-03-15 22:06:51,083] [INFO] Target genome list was writen to OceanDNA-b12609/target_genomes.txt
[2023-03-15 22:06:51,098] [INFO] Task started: fastANI
[2023-03-15 22:06:51,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg38dc7b6e-8bf3-4045-b330-a09cc687f7d3/OceanDNA-b12609.fa --refList OceanDNA-b12609/target_genomes.txt --output OceanDNA-b12609/fastani_result.tsv --threads 1
[2023-03-15 22:07:03,689] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:03,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:07:03,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:07:03,692] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 22:07:03,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 22:07:03,692] [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
Acidiluteibacter ferrifornacis	strain=S-15	GCA_009909615.1	2692424	2692424	type	True	98.3564	621	653	95	conclusive
--------------------------------------------------------------------------------
[2023-03-15 22:07:03,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12609/tc_result.tsv
[2023-03-15 22:07:03,695] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:07:03,695] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:07:03,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference/checkm_data
[2023-03-15 22:07:03,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:07:03,701] [INFO] Task started: CheckM
[2023-03-15 22:07:03,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12609/checkm_input OceanDNA-b12609/checkm_result
[2023-03-15 22:07:43,767] [INFO] Task succeeded: CheckM
[2023-03-15 22:07:43,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:07:43,822] [INFO] ===== Completeness check finished =====
[2023-03-15 22:07:43,822] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:07:43,822] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12609/markers.fasta)
[2023-03-15 22:07:43,823] [INFO] Task started: Blastn
[2023-03-15 22:07:43,823] [INFO] Running command: blastn -query OceanDNA-b12609/markers.fasta -db /var/lib/cwl/stg95567db5-4aaa-4c7e-b63b-9f348bcdb2e3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:07:44,463] [INFO] Task succeeded: Blastn
[2023-03-15 22:07:44,476] [INFO] Selected 25 target genomes.
[2023-03-15 22:07:44,476] [INFO] Target genome list was writen to OceanDNA-b12609/target_genomes_gtdb.txt
[2023-03-15 22:07:44,581] [INFO] Task started: fastANI
[2023-03-15 22:07:44,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg38dc7b6e-8bf3-4045-b330-a09cc687f7d3/OceanDNA-b12609.fa --refList OceanDNA-b12609/target_genomes_gtdb.txt --output OceanDNA-b12609/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:07:57,121] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:57,124] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:07:57,124] [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_009909615.1	s__Acidiluteibacter ferrifornacis	98.3564	621	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Acidiluteibacter	95.0	97.97	97.97	0.91	0.91	2	conclusive
GCA_018402765.1	s__Acidiluteibacter sp018402765	78.7359	155	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Acidiluteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:07:57,133] [INFO] GTDB search result was written to OceanDNA-b12609/result_gtdb.tsv
[2023-03-15 22:07:57,144] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:07:57,154] [INFO] DFAST_QC result json was written to OceanDNA-b12609/dqc_result.json
[2023-03-15 22:07:57,154] [INFO] DFAST_QC completed!
[2023-03-15 22:07:57,154] [INFO] Total running time: 0h1m22s