[2023-03-18 04:30:29,525] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:30:29,525] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:30:29,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference
[2023-03-18 04:30:30,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:30:30,624] [INFO] Task started: Prodigal
[2023-03-18 04:30:30,624] [INFO] Running command: cat /var/lib/cwl/stg94d0876a-ebcb-433b-bfca-56f76bd11cdd/OceanDNA-b12854.fa | prodigal -d OceanDNA-b12854/cds.fna -a OceanDNA-b12854/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:30:42,531] [INFO] Task succeeded: Prodigal
[2023-03-18 04:30:42,531] [INFO] Task started: HMMsearch
[2023-03-18 04:30:42,531] [INFO] Running command: hmmsearch --tblout OceanDNA-b12854/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference/reference_markers.hmm OceanDNA-b12854/protein.faa > /dev/null
[2023-03-18 04:30:42,721] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:30:42,722] [INFO] Found 6/6 markers.
[2023-03-18 04:30:42,738] [INFO] Query marker FASTA was written to OceanDNA-b12854/markers.fasta
[2023-03-18 04:30:42,738] [INFO] Task started: Blastn
[2023-03-18 04:30:42,738] [INFO] Running command: blastn -query OceanDNA-b12854/markers.fasta -db /var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference/reference_markers.fasta -out OceanDNA-b12854/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:30:43,257] [INFO] Task succeeded: Blastn
[2023-03-18 04:30:43,258] [INFO] Selected 33 target genomes.
[2023-03-18 04:30:43,258] [INFO] Target genome list was writen to OceanDNA-b12854/target_genomes.txt
[2023-03-18 04:30:43,272] [INFO] Task started: fastANI
[2023-03-18 04:30:43,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d0876a-ebcb-433b-bfca-56f76bd11cdd/OceanDNA-b12854.fa --refList OceanDNA-b12854/target_genomes.txt --output OceanDNA-b12854/fastani_result.tsv --threads 1
[2023-03-18 04:30:59,925] [INFO] Task succeeded: fastANI
[2023-03-18 04:30:59,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:30:59,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:30:59,925] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:30:59,925] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:30:59,926] [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
--------------------------------------------------------------------------------
[2023-03-18 04:30:59,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12854/tc_result.tsv
[2023-03-18 04:30:59,926] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:30:59,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:30:59,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference/checkm_data
[2023-03-18 04:30:59,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:31:00,006] [INFO] Task started: CheckM
[2023-03-18 04:31:00,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12854/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12854/checkm_input OceanDNA-b12854/checkm_result
[2023-03-18 04:31:34,449] [INFO] Task succeeded: CheckM
[2023-03-18 04:31:34,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:31:34,451] [INFO] ===== Completeness check finished =====
[2023-03-18 04:31:34,451] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:31:34,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12854/markers.fasta)
[2023-03-18 04:31:34,453] [INFO] Task started: Blastn
[2023-03-18 04:31:34,453] [INFO] Running command: blastn -query OceanDNA-b12854/markers.fasta -db /var/lib/cwl/stg8ac7360f-f54b-4871-b027-4d639b7d8fb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12854/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:31:35,179] [INFO] Task succeeded: Blastn
[2023-03-18 04:31:35,180] [INFO] Selected 31 target genomes.
[2023-03-18 04:31:35,180] [INFO] Target genome list was writen to OceanDNA-b12854/target_genomes_gtdb.txt
[2023-03-18 04:31:35,208] [INFO] Task started: fastANI
[2023-03-18 04:31:35,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d0876a-ebcb-433b-bfca-56f76bd11cdd/OceanDNA-b12854.fa --refList OceanDNA-b12854/target_genomes_gtdb.txt --output OceanDNA-b12854/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:31:50,469] [INFO] Task succeeded: fastANI
[2023-03-18 04:31:50,472] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:31:50,472] [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_905478335.1	s__UBA987 sp002292105	83.2564	360	421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA987	95.0	99.89	99.89	0.92	0.92	2	-
GCA_017640445.1	s__UBA987 sp017640445	76.4081	55	421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA987	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:31:50,472] [INFO] GTDB search result was written to OceanDNA-b12854/result_gtdb.tsv
[2023-03-18 04:31:50,472] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:31:50,473] [INFO] DFAST_QC result json was written to OceanDNA-b12854/dqc_result.json
[2023-03-18 04:31:50,473] [INFO] DFAST_QC completed!
[2023-03-18 04:31:50,473] [INFO] Total running time: 0h1m21s