[2023-03-15 05:54:38,679] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:54:38,679] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:54:38,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference
[2023-03-15 05:54:39,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:54:39,778] [INFO] Task started: Prodigal
[2023-03-15 05:54:39,778] [INFO] Running command: cat /var/lib/cwl/stg120ffc51-778f-49be-803c-eb77a1b563f7/OceanDNA-b21441.fa | prodigal -d OceanDNA-b21441/cds.fna -a OceanDNA-b21441/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:54:45,489] [INFO] Task succeeded: Prodigal
[2023-03-15 05:54:45,489] [INFO] Task started: HMMsearch
[2023-03-15 05:54:45,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b21441/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference/reference_markers.hmm OceanDNA-b21441/protein.faa > /dev/null
[2023-03-15 05:54:45,660] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:54:45,661] [INFO] Found 6/6 markers.
[2023-03-15 05:54:45,694] [INFO] Query marker FASTA was written to OceanDNA-b21441/markers.fasta
[2023-03-15 05:54:45,695] [INFO] Task started: Blastn
[2023-03-15 05:54:45,695] [INFO] Running command: blastn -query OceanDNA-b21441/markers.fasta -db /var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference/reference_markers.fasta -out OceanDNA-b21441/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:54:46,253] [INFO] Task succeeded: Blastn
[2023-03-15 05:54:46,263] [INFO] Selected 12 target genomes.
[2023-03-15 05:54:46,263] [INFO] Target genome list was writen to OceanDNA-b21441/target_genomes.txt
[2023-03-15 05:54:46,268] [INFO] Task started: fastANI
[2023-03-15 05:54:46,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg120ffc51-778f-49be-803c-eb77a1b563f7/OceanDNA-b21441.fa --refList OceanDNA-b21441/target_genomes.txt --output OceanDNA-b21441/fastani_result.tsv --threads 1
[2023-03-15 05:54:52,492] [INFO] Task succeeded: fastANI
[2023-03-15 05:54:52,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:54:52,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:54:52,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:54:52,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:54:52,493] [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
--------------------------------------------------------------------------------
[2023-03-15 05:54:52,503] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21441/tc_result.tsv
[2023-03-15 05:54:52,524] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:54:52,524] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:54:52,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference/checkm_data
[2023-03-15 05:54:52,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:54:52,690] [INFO] Task started: CheckM
[2023-03-15 05:54:52,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21441/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21441/checkm_input OceanDNA-b21441/checkm_result
[2023-03-15 05:55:14,328] [INFO] Task succeeded: CheckM
[2023-03-15 05:55:14,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.91%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:55:14,366] [INFO] ===== Completeness check finished =====
[2023-03-15 05:55:14,366] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:55:14,366] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21441/markers.fasta)
[2023-03-15 05:55:14,367] [INFO] Task started: Blastn
[2023-03-15 05:55:14,367] [INFO] Running command: blastn -query OceanDNA-b21441/markers.fasta -db /var/lib/cwl/stgef0a79ed-f9b7-4a4b-bd66-0ba61f836696/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21441/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:55:15,227] [INFO] Task succeeded: Blastn
[2023-03-15 05:55:15,236] [INFO] Selected 16 target genomes.
[2023-03-15 05:55:15,236] [INFO] Target genome list was writen to OceanDNA-b21441/target_genomes_gtdb.txt
[2023-03-15 05:55:15,251] [INFO] Task started: fastANI
[2023-03-15 05:55:15,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg120ffc51-778f-49be-803c-eb77a1b563f7/OceanDNA-b21441.fa --refList OceanDNA-b21441/target_genomes_gtdb.txt --output OceanDNA-b21441/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:55:20,256] [INFO] Task succeeded: fastANI
[2023-03-15 05:55:20,258] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:55:20,258] [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_013204395.1	s__JABMNZ01 sp013204395	82.8504	166	226	d__Bacteria;p__Patescibacteria;c__ABY1;o__SG8-24;f__GWF2-40-263;g__JABMNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844925.1	s__JABMNZ01 sp016844925	77.2448	61	226	d__Bacteria;p__Patescibacteria;c__ABY1;o__SG8-24;f__GWF2-40-263;g__JABMNZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:55:20,392] [INFO] GTDB search result was written to OceanDNA-b21441/result_gtdb.tsv
[2023-03-15 05:55:20,408] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:55:20,416] [INFO] DFAST_QC result json was written to OceanDNA-b21441/dqc_result.json
[2023-03-15 05:55:20,417] [INFO] DFAST_QC completed!
[2023-03-15 05:55:20,417] [INFO] Total running time: 0h0m42s