[2023-03-18 23:11:06,972] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,972] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference
[2023-03-18 23:11:08,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,166] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,166] [INFO] Running command: cat /var/lib/cwl/stg89314cbc-55df-4893-8b7a-24f72cffe346/OceanDNA-b21008.fa | prodigal -d OceanDNA-b21008/cds.fna -a OceanDNA-b21008/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:21,532] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:21,532] [INFO] Task started: HMMsearch
[2023-03-18 23:11:21,532] [INFO] Running command: hmmsearch --tblout OceanDNA-b21008/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference/reference_markers.hmm OceanDNA-b21008/protein.faa > /dev/null
[2023-03-18 23:11:21,740] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:21,740] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg89314cbc-55df-4893-8b7a-24f72cffe346/OceanDNA-b21008.fa]
[2023-03-18 23:11:21,765] [INFO] Query marker FASTA was written to OceanDNA-b21008/markers.fasta
[2023-03-18 23:11:21,765] [INFO] Task started: Blastn
[2023-03-18 23:11:21,765] [INFO] Running command: blastn -query OceanDNA-b21008/markers.fasta -db /var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference/reference_markers.fasta -out OceanDNA-b21008/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:22,325] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:22,326] [INFO] Selected 15 target genomes.
[2023-03-18 23:11:22,326] [INFO] Target genome list was writen to OceanDNA-b21008/target_genomes.txt
[2023-03-18 23:11:22,335] [INFO] Task started: fastANI
[2023-03-18 23:11:22,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg89314cbc-55df-4893-8b7a-24f72cffe346/OceanDNA-b21008.fa --refList OceanDNA-b21008/target_genomes.txt --output OceanDNA-b21008/fastani_result.tsv --threads 1
[2023-03-18 23:11:36,284] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:36,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:36,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:36,284] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:36,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:36,285] [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 23:11:36,285] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21008/tc_result.tsv
[2023-03-18 23:11:36,285] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:36,285] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:36,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference/checkm_data
[2023-03-18 23:11:36,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:36,293] [INFO] Task started: CheckM
[2023-03-18 23:11:36,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21008/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21008/checkm_input OceanDNA-b21008/checkm_result
[2023-03-18 23:12:13,553] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:13,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:13,557] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:13,557] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:13,557] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21008/markers.fasta)
[2023-03-18 23:12:13,558] [INFO] Task started: Blastn
[2023-03-18 23:12:13,558] [INFO] Running command: blastn -query OceanDNA-b21008/markers.fasta -db /var/lib/cwl/stg674d8a73-4ea0-43bb-8284-e0b5118931f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21008/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:14,399] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:14,400] [INFO] Selected 17 target genomes.
[2023-03-18 23:12:14,400] [INFO] Target genome list was writen to OceanDNA-b21008/target_genomes_gtdb.txt
[2023-03-18 23:12:14,414] [INFO] Task started: fastANI
[2023-03-18 23:12:14,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg89314cbc-55df-4893-8b7a-24f72cffe346/OceanDNA-b21008.fa --refList OceanDNA-b21008/target_genomes_gtdb.txt --output OceanDNA-b21008/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:26,449] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:26,451] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:26,451] [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_012960035.1	s__DUBZ01 sp012960035	96.005	476	494	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__DUBZ01	95.0	99.83	99.83	0.93	0.93	2	conclusive
--------------------------------------------------------------------------------
[2023-03-18 23:12:26,451] [INFO] GTDB search result was written to OceanDNA-b21008/result_gtdb.tsv
[2023-03-18 23:12:26,451] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:26,452] [INFO] DFAST_QC result json was written to OceanDNA-b21008/dqc_result.json
[2023-03-18 23:12:26,452] [INFO] DFAST_QC completed!
[2023-03-18 23:12:26,452] [INFO] Total running time: 0h1m19s