[2023-03-16 06:24:06,023] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:24:06,023] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:24:06,024] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference
[2023-03-16 06:24:07,107] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:24:07,107] [INFO] Task started: Prodigal
[2023-03-16 06:24:07,107] [INFO] Running command: cat /var/lib/cwl/stgff22e9b1-c111-46bc-b1cd-00440d2cfa04/OceanDNA-b11563.fa | prodigal -d OceanDNA-b11563/cds.fna -a OceanDNA-b11563/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:24:12,517] [INFO] Task succeeded: Prodigal
[2023-03-16 06:24:12,517] [INFO] Task started: HMMsearch
[2023-03-16 06:24:12,517] [INFO] Running command: hmmsearch --tblout OceanDNA-b11563/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference/reference_markers.hmm OceanDNA-b11563/protein.faa > /dev/null
[2023-03-16 06:24:12,688] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:24:12,689] [INFO] Found 6/6 markers.
[2023-03-16 06:24:12,698] [INFO] Query marker FASTA was written to OceanDNA-b11563/markers.fasta
[2023-03-16 06:24:12,699] [INFO] Task started: Blastn
[2023-03-16 06:24:12,699] [INFO] Running command: blastn -query OceanDNA-b11563/markers.fasta -db /var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference/reference_markers.fasta -out OceanDNA-b11563/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:24:13,244] [INFO] Task succeeded: Blastn
[2023-03-16 06:24:13,244] [INFO] Selected 30 target genomes.
[2023-03-16 06:24:13,245] [INFO] Target genome list was writen to OceanDNA-b11563/target_genomes.txt
[2023-03-16 06:24:13,256] [INFO] Task started: fastANI
[2023-03-16 06:24:13,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgff22e9b1-c111-46bc-b1cd-00440d2cfa04/OceanDNA-b11563.fa --refList OceanDNA-b11563/target_genomes.txt --output OceanDNA-b11563/fastani_result.tsv --threads 1
[2023-03-16 06:24:27,908] [INFO] Task succeeded: fastANI
[2023-03-16 06:24:27,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:24:27,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:24:27,909] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:24:27,909] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:24:27,909] [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
--------------------------------------------------------------------------------
[2023-03-16 06:24:27,909] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11563/tc_result.tsv
[2023-03-16 06:24:27,909] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:24:27,909] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:24:27,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference/checkm_data
[2023-03-16 06:24:27,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:24:28,012] [INFO] Task started: CheckM
[2023-03-16 06:24:28,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11563/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11563/checkm_input OceanDNA-b11563/checkm_result
[2023-03-16 06:24:47,530] [INFO] Task succeeded: CheckM
[2023-03-16 06:24:47,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:24:47,532] [INFO] ===== Completeness check finished =====
[2023-03-16 06:24:47,532] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:24:47,533] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11563/markers.fasta)
[2023-03-16 06:24:47,534] [INFO] Task started: Blastn
[2023-03-16 06:24:47,534] [INFO] Running command: blastn -query OceanDNA-b11563/markers.fasta -db /var/lib/cwl/stgc0c08ebb-d972-4029-9f43-857ff795779a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11563/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:24:48,423] [INFO] Task succeeded: Blastn
[2023-03-16 06:24:48,424] [INFO] Selected 27 target genomes.
[2023-03-16 06:24:48,424] [INFO] Target genome list was writen to OceanDNA-b11563/target_genomes_gtdb.txt
[2023-03-16 06:24:48,451] [INFO] Task started: fastANI
[2023-03-16 06:24:48,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgff22e9b1-c111-46bc-b1cd-00440d2cfa04/OceanDNA-b11563.fa --refList OceanDNA-b11563/target_genomes_gtdb.txt --output OceanDNA-b11563/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:24:56,797] [INFO] Task succeeded: fastANI
[2023-03-16 06:24:56,801] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:24:56,801] [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_002714185.1	s__SP256 sp002714185	77.2311	86	248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713285.1	s__SP256 sp002713285	77.214	85	248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	77.1631	82	248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	76.8562	71	248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.6759	65	248	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:24:56,801] [INFO] GTDB search result was written to OceanDNA-b11563/result_gtdb.tsv
[2023-03-16 06:24:56,801] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:24:56,802] [INFO] DFAST_QC result json was written to OceanDNA-b11563/dqc_result.json
[2023-03-16 06:24:56,802] [INFO] DFAST_QC completed!
[2023-03-16 06:24:56,802] [INFO] Total running time: 0h0m51s