[2023-03-17 08:39:27,187] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,187] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,187] [INFO] DQC Reference Directory: /var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference
[2023-03-17 08:39:28,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,404] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,404] [INFO] Running command: cat /var/lib/cwl/stg566c8680-580f-48e8-90b0-0e9a337b0039/OceanDNA-b24179.fa | prodigal -d OceanDNA-b24179/cds.fna -a OceanDNA-b24179/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:32,677] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:32,678] [INFO] Task started: HMMsearch
[2023-03-17 08:39:32,678] [INFO] Running command: hmmsearch --tblout OceanDNA-b24179/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference/reference_markers.hmm OceanDNA-b24179/protein.faa > /dev/null
[2023-03-17 08:39:32,816] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:32,817] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg566c8680-580f-48e8-90b0-0e9a337b0039/OceanDNA-b24179.fa]
[2023-03-17 08:39:32,826] [INFO] Query marker FASTA was written to OceanDNA-b24179/markers.fasta
[2023-03-17 08:39:32,826] [INFO] Task started: Blastn
[2023-03-17 08:39:32,826] [INFO] Running command: blastn -query OceanDNA-b24179/markers.fasta -db /var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference/reference_markers.fasta -out OceanDNA-b24179/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:33,325] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:33,327] [INFO] Selected 17 target genomes.
[2023-03-17 08:39:33,327] [INFO] Target genome list was writen to OceanDNA-b24179/target_genomes.txt
[2023-03-17 08:39:33,711] [INFO] Task started: fastANI
[2023-03-17 08:39:33,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg566c8680-580f-48e8-90b0-0e9a337b0039/OceanDNA-b24179.fa --refList OceanDNA-b24179/target_genomes.txt --output OceanDNA-b24179/fastani_result.tsv --threads 1
[2023-03-17 08:39:38,908] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:38,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:39:38,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:39:38,909] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:39:38,909] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:39:38,909] [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
--------------------------------------------------------------------------------
[2023-03-17 08:39:38,910] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24179/tc_result.tsv
[2023-03-17 08:39:38,911] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:39:38,911] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:38,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference/checkm_data
[2023-03-17 08:39:38,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:39,052] [INFO] Task started: CheckM
[2023-03-17 08:39:39,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24179/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24179/checkm_input OceanDNA-b24179/checkm_result
[2023-03-17 08:39:55,854] [INFO] Task succeeded: CheckM
[2023-03-17 08:39:55,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:39:55,858] [INFO] ===== Completeness check finished =====
[2023-03-17 08:39:55,858] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:39:55,858] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24179/markers.fasta)
[2023-03-17 08:39:55,859] [INFO] Task started: Blastn
[2023-03-17 08:39:55,859] [INFO] Running command: blastn -query OceanDNA-b24179/markers.fasta -db /var/lib/cwl/stgd47665fe-bb71-42d1-8c65-329aacd08ed2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24179/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:56,525] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:56,527] [INFO] Selected 12 target genomes.
[2023-03-17 08:39:56,527] [INFO] Target genome list was writen to OceanDNA-b24179/target_genomes_gtdb.txt
[2023-03-17 08:39:57,021] [INFO] Task started: fastANI
[2023-03-17 08:39:57,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg566c8680-580f-48e8-90b0-0e9a337b0039/OceanDNA-b24179.fa --refList OceanDNA-b24179/target_genomes_gtdb.txt --output OceanDNA-b24179/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:39:59,096] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:59,101] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:39:59,101] [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_902607475.1	s__GCA-002720895 sp902607475	83.998	144	248	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711715.1	s__GCA-002720895 sp002711715	82.8061	103	248	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937775.1	s__GCA-002720895 sp002937775	80.5503	153	248	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.14	99.14	0.75	0.75	2	-
GCA_002717245.1	s__GCA-002720895 sp002717245	80.4327	201	248	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	-
GCA_002720895.1	s__GCA-002720895 sp002720895	80.2242	119	248	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:39:59,103] [INFO] GTDB search result was written to OceanDNA-b24179/result_gtdb.tsv
[2023-03-17 08:39:59,104] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:39:59,105] [INFO] DFAST_QC result json was written to OceanDNA-b24179/dqc_result.json
[2023-03-17 08:39:59,106] [INFO] DFAST_QC completed!
[2023-03-17 08:39:59,106] [INFO] Total running time: 0h0m32s