[2023-03-16 06:33:31,991] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:33:31,992] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:33:31,992] [INFO] DQC Reference Directory: /var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference
[2023-03-16 06:33:33,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:33:33,166] [INFO] Task started: Prodigal
[2023-03-16 06:33:33,166] [INFO] Running command: cat /var/lib/cwl/stg920e903e-a85b-4c8a-919a-8e394b279627/OceanDNA-b22613.fa | prodigal -d OceanDNA-b22613/cds.fna -a OceanDNA-b22613/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:33:54,725] [INFO] Task succeeded: Prodigal
[2023-03-16 06:33:54,725] [INFO] Task started: HMMsearch
[2023-03-16 06:33:54,725] [INFO] Running command: hmmsearch --tblout OceanDNA-b22613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference/reference_markers.hmm OceanDNA-b22613/protein.faa > /dev/null
[2023-03-16 06:33:54,966] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:33:54,967] [INFO] Found 6/6 markers.
[2023-03-16 06:33:55,001] [INFO] Query marker FASTA was written to OceanDNA-b22613/markers.fasta
[2023-03-16 06:33:55,002] [INFO] Task started: Blastn
[2023-03-16 06:33:55,003] [INFO] Running command: blastn -query OceanDNA-b22613/markers.fasta -db /var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference/reference_markers.fasta -out OceanDNA-b22613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:33:55,561] [INFO] Task succeeded: Blastn
[2023-03-16 06:33:55,562] [INFO] Selected 6 target genomes.
[2023-03-16 06:33:55,562] [INFO] Target genome list was writen to OceanDNA-b22613/target_genomes.txt
[2023-03-16 06:33:55,566] [INFO] Task started: fastANI
[2023-03-16 06:33:55,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg920e903e-a85b-4c8a-919a-8e394b279627/OceanDNA-b22613.fa --refList OceanDNA-b22613/target_genomes.txt --output OceanDNA-b22613/fastani_result.tsv --threads 1
[2023-03-16 06:33:58,916] [INFO] Task succeeded: fastANI
[2023-03-16 06:33:58,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:33:58,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:33:58,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:33:58,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:33:58,917] [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 06:33:58,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22613/tc_result.tsv
[2023-03-16 06:33:58,917] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:33:58,917] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:33:58,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference/checkm_data
[2023-03-16 06:33:58,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:33:58,927] [INFO] Task started: CheckM
[2023-03-16 06:33:58,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22613/checkm_input OceanDNA-b22613/checkm_result
[2023-03-16 06:34:54,690] [INFO] Task succeeded: CheckM
[2023-03-16 06:34:54,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.75%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:34:54,694] [INFO] ===== Completeness check finished =====
[2023-03-16 06:34:54,694] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:34:54,694] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22613/markers.fasta)
[2023-03-16 06:34:54,695] [INFO] Task started: Blastn
[2023-03-16 06:34:54,695] [INFO] Running command: blastn -query OceanDNA-b22613/markers.fasta -db /var/lib/cwl/stgd797005f-997a-4f57-97c3-bd913758012f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:34:55,674] [INFO] Task succeeded: Blastn
[2023-03-16 06:34:55,675] [INFO] Selected 16 target genomes.
[2023-03-16 06:34:55,675] [INFO] Target genome list was writen to OceanDNA-b22613/target_genomes_gtdb.txt
[2023-03-16 06:34:55,686] [INFO] Task started: fastANI
[2023-03-16 06:34:55,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg920e903e-a85b-4c8a-919a-8e394b279627/OceanDNA-b22613.fa --refList OceanDNA-b22613/target_genomes_gtdb.txt --output OceanDNA-b22613/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:35:08,335] [INFO] Task succeeded: fastANI
[2023-03-16 06:35:08,338] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:35:08,338] [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_002724245.1	s__UBA9264 sp002724245	92.8989	881	931	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA9264	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709225.1	s__UBA9264 sp002709225	83.9965	658	931	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA9264	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702965.1	s__UBA9264 sp002702965	77.178	167	931	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA9264	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:35:08,338] [INFO] GTDB search result was written to OceanDNA-b22613/result_gtdb.tsv
[2023-03-16 06:35:08,339] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:35:08,339] [INFO] DFAST_QC result json was written to OceanDNA-b22613/dqc_result.json
[2023-03-16 06:35:08,339] [INFO] DFAST_QC completed!
[2023-03-16 06:35:08,339] [INFO] Total running time: 0h1m36s