[2023-03-17 10:48:45,636] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,637] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference
[2023-03-17 10:48:46,818] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,818] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,819] [INFO] Running command: cat /var/lib/cwl/stgd55352b3-bd21-4c86-bfb4-aa5831e94870/OceanDNA-b10475.fa | prodigal -d OceanDNA-b10475/cds.fna -a OceanDNA-b10475/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:57,830] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:57,830] [INFO] Task started: HMMsearch
[2023-03-17 10:48:57,830] [INFO] Running command: hmmsearch --tblout OceanDNA-b10475/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference/reference_markers.hmm OceanDNA-b10475/protein.faa > /dev/null
[2023-03-17 10:48:58,017] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:58,017] [INFO] Found 6/6 markers.
[2023-03-17 10:48:58,030] [INFO] Query marker FASTA was written to OceanDNA-b10475/markers.fasta
[2023-03-17 10:48:58,030] [INFO] Task started: Blastn
[2023-03-17 10:48:58,030] [INFO] Running command: blastn -query OceanDNA-b10475/markers.fasta -db /var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference/reference_markers.fasta -out OceanDNA-b10475/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:58,575] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:58,576] [INFO] Selected 40 target genomes.
[2023-03-17 10:48:58,577] [INFO] Target genome list was writen to OceanDNA-b10475/target_genomes.txt
[2023-03-17 10:48:58,695] [INFO] Task started: fastANI
[2023-03-17 10:48:58,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55352b3-bd21-4c86-bfb4-aa5831e94870/OceanDNA-b10475.fa --refList OceanDNA-b10475/target_genomes.txt --output OceanDNA-b10475/fastani_result.tsv --threads 1
[2023-03-17 10:49:23,823] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:23,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:23,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:23,823] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:23,823] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:23,823] [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 10:49:23,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10475/tc_result.tsv
[2023-03-17 10:49:23,824] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:23,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:23,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference/checkm_data
[2023-03-17 10:49:23,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:23,848] [INFO] Task started: CheckM
[2023-03-17 10:49:23,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10475/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10475/checkm_input OceanDNA-b10475/checkm_result
[2023-03-17 10:49:56,872] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:56,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:56,874] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:56,874] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:56,874] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10475/markers.fasta)
[2023-03-17 10:49:56,875] [INFO] Task started: Blastn
[2023-03-17 10:49:56,875] [INFO] Running command: blastn -query OceanDNA-b10475/markers.fasta -db /var/lib/cwl/stg43cf9830-d511-4573-9afb-36978cea739e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10475/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:57,704] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:57,705] [INFO] Selected 33 target genomes.
[2023-03-17 10:49:57,705] [INFO] Target genome list was writen to OceanDNA-b10475/target_genomes_gtdb.txt
[2023-03-17 10:49:58,168] [INFO] Task started: fastANI
[2023-03-17 10:49:58,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55352b3-bd21-4c86-bfb4-aa5831e94870/OceanDNA-b10475.fa --refList OceanDNA-b10475/target_genomes_gtdb.txt --output OceanDNA-b10475/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:50:11,721] [INFO] Task succeeded: fastANI
[2023-03-17 10:50:11,724] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:50:11,724] [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_009886755.1	s__UBA11891 sp009886755	98.9184	408	443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	99.16	98.70	0.90	0.89	3	conclusive
GCA_003533785.1	s__UBA11891 sp003533785	77.1533	113	443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	99.52	99.52	0.75	0.75	2	-
GCA_011524905.1	s__UBA11891 sp011524905	76.7974	105	443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:50:11,725] [INFO] GTDB search result was written to OceanDNA-b10475/result_gtdb.tsv
[2023-03-17 10:50:11,725] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:50:11,725] [INFO] DFAST_QC result json was written to OceanDNA-b10475/dqc_result.json
[2023-03-17 10:50:11,726] [INFO] DFAST_QC completed!
[2023-03-17 10:50:11,726] [INFO] Total running time: 0h1m26s