[2023-03-17 10:48:47,651] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:47,651] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:47,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference
[2023-03-17 10:48:48,800] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:48,801] [INFO] Task started: Prodigal
[2023-03-17 10:48:48,801] [INFO] Running command: cat /var/lib/cwl/stg142423c4-894b-4a3b-bd2e-adfece4a66e4/OceanDNA-b14104.fa | prodigal -d OceanDNA-b14104/cds.fna -a OceanDNA-b14104/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:57,229] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:57,230] [INFO] Task started: HMMsearch
[2023-03-17 10:48:57,230] [INFO] Running command: hmmsearch --tblout OceanDNA-b14104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference/reference_markers.hmm OceanDNA-b14104/protein.faa > /dev/null
[2023-03-17 10:48:57,430] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:57,430] [INFO] Found 6/6 markers.
[2023-03-17 10:48:57,445] [INFO] Query marker FASTA was written to OceanDNA-b14104/markers.fasta
[2023-03-17 10:48:57,446] [INFO] Task started: Blastn
[2023-03-17 10:48:57,446] [INFO] Running command: blastn -query OceanDNA-b14104/markers.fasta -db /var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference/reference_markers.fasta -out OceanDNA-b14104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:57,960] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:57,961] [INFO] Selected 13 target genomes.
[2023-03-17 10:48:57,962] [INFO] Target genome list was writen to OceanDNA-b14104/target_genomes.txt
[2023-03-17 10:48:57,970] [INFO] Task started: fastANI
[2023-03-17 10:48:57,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg142423c4-894b-4a3b-bd2e-adfece4a66e4/OceanDNA-b14104.fa --refList OceanDNA-b14104/target_genomes.txt --output OceanDNA-b14104/fastani_result.tsv --threads 1
[2023-03-17 10:49:02,714] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:02,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:02,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:02,715] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:02,715] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:02,715] [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 10:49:02,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14104/tc_result.tsv
[2023-03-17 10:49:02,716] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:02,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:02,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference/checkm_data
[2023-03-17 10:49:02,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:02,731] [INFO] Task started: CheckM
[2023-03-17 10:49:02,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14104/checkm_input OceanDNA-b14104/checkm_result
[2023-03-17 10:49:29,307] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:29,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.84%
Contamintation: 4.92%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:29,309] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:29,309] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:29,309] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14104/markers.fasta)
[2023-03-17 10:49:29,310] [INFO] Task started: Blastn
[2023-03-17 10:49:29,311] [INFO] Running command: blastn -query OceanDNA-b14104/markers.fasta -db /var/lib/cwl/stg473a6652-8b8d-4478-96e2-90675e1ec384/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:30,050] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:30,051] [INFO] Selected 13 target genomes.
[2023-03-17 10:49:30,051] [INFO] Target genome list was writen to OceanDNA-b14104/target_genomes_gtdb.txt
[2023-03-17 10:49:30,309] [INFO] Task started: fastANI
[2023-03-17 10:49:30,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg142423c4-894b-4a3b-bd2e-adfece4a66e4/OceanDNA-b14104.fa --refList OceanDNA-b14104/target_genomes_gtdb.txt --output OceanDNA-b14104/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:35,270] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:35,273] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:35,274] [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_009391195.1	s__GCA-002712965 sp009391195	98.7731	313	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002696685.1	s__GCA-002712965 sp002696685	86.4387	405	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	98.93	98.49	0.85	0.81	3	-
GCA_009392815.1	s__GCA-002712965 sp009392815	80.6976	292	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	99.65	99.65	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:35,274] [INFO] GTDB search result was written to OceanDNA-b14104/result_gtdb.tsv
[2023-03-17 10:49:35,274] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:35,274] [INFO] DFAST_QC result json was written to OceanDNA-b14104/dqc_result.json
[2023-03-17 10:49:35,275] [INFO] DFAST_QC completed!
[2023-03-17 10:49:35,275] [INFO] Total running time: 0h0m48s