[2023-03-16 20:04:44,490] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:04:44,490] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:04:44,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference
[2023-03-16 20:04:45,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:04:45,593] [INFO] Task started: Prodigal
[2023-03-16 20:04:45,593] [INFO] Running command: cat /var/lib/cwl/stg6930a328-95df-4ee1-b3ab-a301daf455db/OceanDNA-b15651.fa | prodigal -d OceanDNA-b15651/cds.fna -a OceanDNA-b15651/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:04:53,051] [INFO] Task succeeded: Prodigal
[2023-03-16 20:04:53,052] [INFO] Task started: HMMsearch
[2023-03-16 20:04:53,052] [INFO] Running command: hmmsearch --tblout OceanDNA-b15651/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference/reference_markers.hmm OceanDNA-b15651/protein.faa > /dev/null
[2023-03-16 20:04:53,333] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:04:53,333] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6930a328-95df-4ee1-b3ab-a301daf455db/OceanDNA-b15651.fa]
[2023-03-16 20:04:53,349] [INFO] Query marker FASTA was written to OceanDNA-b15651/markers.fasta
[2023-03-16 20:04:53,354] [INFO] Task started: Blastn
[2023-03-16 20:04:53,354] [INFO] Running command: blastn -query OceanDNA-b15651/markers.fasta -db /var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference/reference_markers.fasta -out OceanDNA-b15651/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:04:54,389] [INFO] Task succeeded: Blastn
[2023-03-16 20:04:54,390] [INFO] Selected 7 target genomes.
[2023-03-16 20:04:54,390] [INFO] Target genome list was writen to OceanDNA-b15651/target_genomes.txt
[2023-03-16 20:04:54,396] [INFO] Task started: fastANI
[2023-03-16 20:04:54,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg6930a328-95df-4ee1-b3ab-a301daf455db/OceanDNA-b15651.fa --refList OceanDNA-b15651/target_genomes.txt --output OceanDNA-b15651/fastani_result.tsv --threads 1
[2023-03-16 20:04:58,099] [INFO] Task succeeded: fastANI
[2023-03-16 20:04:58,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:04:58,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:04:58,100] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:04:58,100] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:04:58,100] [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 20:04:58,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15651/tc_result.tsv
[2023-03-16 20:04:58,100] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:04:58,100] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:04:58,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference/checkm_data
[2023-03-16 20:04:58,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:04:58,498] [INFO] Task started: CheckM
[2023-03-16 20:04:58,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15651/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15651/checkm_input OceanDNA-b15651/checkm_result
[2023-03-16 20:05:26,767] [INFO] Task succeeded: CheckM
[2023-03-16 20:05:26,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:05:26,769] [INFO] ===== Completeness check finished =====
[2023-03-16 20:05:26,770] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:05:26,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15651/markers.fasta)
[2023-03-16 20:05:26,772] [INFO] Task started: Blastn
[2023-03-16 20:05:26,772] [INFO] Running command: blastn -query OceanDNA-b15651/markers.fasta -db /var/lib/cwl/stg1422dde5-61d6-41d1-a665-7b86cb22f326/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15651/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:05:28,189] [INFO] Task succeeded: Blastn
[2023-03-16 20:05:28,190] [INFO] Selected 14 target genomes.
[2023-03-16 20:05:28,190] [INFO] Target genome list was writen to OceanDNA-b15651/target_genomes_gtdb.txt
[2023-03-16 20:05:28,212] [INFO] Task started: fastANI
[2023-03-16 20:05:28,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg6930a328-95df-4ee1-b3ab-a301daf455db/OceanDNA-b15651.fa --refList OceanDNA-b15651/target_genomes_gtdb.txt --output OceanDNA-b15651/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:05:35,132] [INFO] Task succeeded: fastANI
[2023-03-16 20:05:35,135] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 20:05:35,136] [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_002716645.1	s__UBA3495 sp002716645	97.917	203	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA3495	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_009392775.1	s__UBA3495 sp009392775	97.7759	242	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA3495	95.0	98.80	98.80	0.63	0.63	2	inconclusive
GCA_002724585.1	s__UBA3495 sp002724585	83.3716	276	409	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA3495	95.0	99.34	99.34	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:05:35,136] [INFO] GTDB search result was written to OceanDNA-b15651/result_gtdb.tsv
[2023-03-16 20:05:35,136] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:05:35,137] [INFO] DFAST_QC result json was written to OceanDNA-b15651/dqc_result.json
[2023-03-16 20:05:35,137] [INFO] DFAST_QC completed!
[2023-03-16 20:05:35,137] [INFO] Total running time: 0h0m51s