[2023-03-18 02:48:49,385] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:49,386] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:49,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference
[2023-03-18 02:48:50,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:50,522] [INFO] Task started: Prodigal
[2023-03-18 02:48:50,522] [INFO] Running command: cat /var/lib/cwl/stgc946a197-813c-4268-ab89-a624a11e39f3/OceanDNA-b5487.fa | prodigal -d OceanDNA-b5487/cds.fna -a OceanDNA-b5487/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:48:55,220] [INFO] Task succeeded: Prodigal
[2023-03-18 02:48:55,220] [INFO] Task started: HMMsearch
[2023-03-18 02:48:55,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b5487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference/reference_markers.hmm OceanDNA-b5487/protein.faa > /dev/null
[2023-03-18 02:48:55,346] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:48:55,347] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc946a197-813c-4268-ab89-a624a11e39f3/OceanDNA-b5487.fa]
[2023-03-18 02:48:55,357] [INFO] Query marker FASTA was written to OceanDNA-b5487/markers.fasta
[2023-03-18 02:48:55,357] [INFO] Task started: Blastn
[2023-03-18 02:48:55,357] [INFO] Running command: blastn -query OceanDNA-b5487/markers.fasta -db /var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference/reference_markers.fasta -out OceanDNA-b5487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:48:55,790] [INFO] Task succeeded: Blastn
[2023-03-18 02:48:55,791] [INFO] Selected 8 target genomes.
[2023-03-18 02:48:55,791] [INFO] Target genome list was writen to OceanDNA-b5487/target_genomes.txt
[2023-03-18 02:48:55,796] [INFO] Task started: fastANI
[2023-03-18 02:48:55,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgc946a197-813c-4268-ab89-a624a11e39f3/OceanDNA-b5487.fa --refList OceanDNA-b5487/target_genomes.txt --output OceanDNA-b5487/fastani_result.tsv --threads 1
[2023-03-18 02:48:59,766] [INFO] Task succeeded: fastANI
[2023-03-18 02:48:59,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:48:59,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:48:59,767] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:48:59,767] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:48:59,767] [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 02:48:59,767] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5487/tc_result.tsv
[2023-03-18 02:48:59,767] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:48:59,768] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:48:59,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference/checkm_data
[2023-03-18 02:48:59,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:48:59,773] [INFO] Task started: CheckM
[2023-03-18 02:48:59,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5487/checkm_input OceanDNA-b5487/checkm_result
[2023-03-18 02:49:19,652] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:19,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:19,654] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:19,654] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:19,654] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5487/markers.fasta)
[2023-03-18 02:49:19,655] [INFO] Task started: Blastn
[2023-03-18 02:49:19,655] [INFO] Running command: blastn -query OceanDNA-b5487/markers.fasta -db /var/lib/cwl/stg71f3894b-80d4-4f41-b775-143d94b90195/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:20,101] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:20,101] [INFO] Selected 11 target genomes.
[2023-03-18 02:49:20,102] [INFO] Target genome list was writen to OceanDNA-b5487/target_genomes_gtdb.txt
[2023-03-18 02:49:20,214] [INFO] Task started: fastANI
[2023-03-18 02:49:20,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgc946a197-813c-4268-ab89-a624a11e39f3/OceanDNA-b5487.fa --refList OceanDNA-b5487/target_genomes_gtdb.txt --output OceanDNA-b5487/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:49:25,070] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:25,073] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:49:25,073] [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_002480215.1	s__UBA952 sp002480215	88.4551	54	62	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_002167775.1	s__UBA952 sp002167775	85.8855	52	62	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:49:25,073] [INFO] GTDB search result was written to OceanDNA-b5487/result_gtdb.tsv
[2023-03-18 02:49:25,073] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:49:25,073] [INFO] DFAST_QC result json was written to OceanDNA-b5487/dqc_result.json
[2023-03-18 02:49:25,074] [INFO] DFAST_QC completed!
[2023-03-18 02:49:25,074] [INFO] Total running time: 0h0m36s