[2023-03-16 01:12:29,295] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,297] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,297] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference
[2023-03-16 01:12:30,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,461] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stg92fb9c1a-e469-45ef-aa08-cd3c427c64a2/OceanDNA-b13518.fa | prodigal -d OceanDNA-b13518/cds.fna -a OceanDNA-b13518/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:37,862] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:37,862] [INFO] Task started: HMMsearch
[2023-03-16 01:12:37,862] [INFO] Running command: hmmsearch --tblout OceanDNA-b13518/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference/reference_markers.hmm OceanDNA-b13518/protein.faa > /dev/null
[2023-03-16 01:12:38,049] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:38,049] [INFO] Found 6/6 markers.
[2023-03-16 01:12:38,107] [INFO] Query marker FASTA was written to OceanDNA-b13518/markers.fasta
[2023-03-16 01:12:38,107] [INFO] Task started: Blastn
[2023-03-16 01:12:38,107] [INFO] Running command: blastn -query OceanDNA-b13518/markers.fasta -db /var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference/reference_markers.fasta -out OceanDNA-b13518/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:38,636] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:38,642] [INFO] Selected 12 target genomes.
[2023-03-16 01:12:38,642] [INFO] Target genome list was writen to OceanDNA-b13518/target_genomes.txt
[2023-03-16 01:12:38,691] [INFO] Task started: fastANI
[2023-03-16 01:12:38,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg92fb9c1a-e469-45ef-aa08-cd3c427c64a2/OceanDNA-b13518.fa --refList OceanDNA-b13518/target_genomes.txt --output OceanDNA-b13518/fastani_result.tsv --threads 1
[2023-03-16 01:12:44,732] [INFO] Task succeeded: fastANI
[2023-03-16 01:12:44,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:12:44,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:12:44,733] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:12:44,733] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:12:44,733] [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 01:12:44,734] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13518/tc_result.tsv
[2023-03-16 01:12:44,734] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:12:44,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:12:44,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference/checkm_data
[2023-03-16 01:12:44,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:12:44,742] [INFO] Task started: CheckM
[2023-03-16 01:12:44,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13518/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13518/checkm_input OceanDNA-b13518/checkm_result
[2023-03-16 01:13:08,489] [INFO] Task succeeded: CheckM
[2023-03-16 01:13:08,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:13:08,561] [INFO] ===== Completeness check finished =====
[2023-03-16 01:13:08,562] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:13:08,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13518/markers.fasta)
[2023-03-16 01:13:08,563] [INFO] Task started: Blastn
[2023-03-16 01:13:08,563] [INFO] Running command: blastn -query OceanDNA-b13518/markers.fasta -db /var/lib/cwl/stgfa7e5c17-1995-45a9-836d-40baed4ae8bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13518/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:09,388] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:09,421] [INFO] Selected 18 target genomes.
[2023-03-16 01:13:09,421] [INFO] Target genome list was writen to OceanDNA-b13518/target_genomes_gtdb.txt
[2023-03-16 01:13:09,759] [INFO] Task started: fastANI
[2023-03-16 01:13:09,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg92fb9c1a-e469-45ef-aa08-cd3c427c64a2/OceanDNA-b13518.fa --refList OceanDNA-b13518/target_genomes_gtdb.txt --output OceanDNA-b13518/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:13:16,753] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:16,757] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:13:16,757] [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_002311455.1	s__UBA11657 sp002311455	84.5789	352	438	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377585.1	s__UBA11657 sp002377585	82.3869	312	438	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.07	98.64	0.89	0.85	4	-
GCA_002346435.1	s__UBA11657 sp002346435	81.96	307	438	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296125.1	s__UBA11657 sp002296125	76.4222	63	438	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.33	99.25	0.80	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-16 01:13:16,764] [INFO] GTDB search result was written to OceanDNA-b13518/result_gtdb.tsv
[2023-03-16 01:13:16,780] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:13:16,788] [INFO] DFAST_QC result json was written to OceanDNA-b13518/dqc_result.json
[2023-03-16 01:13:16,788] [INFO] DFAST_QC completed!
[2023-03-16 01:13:16,788] [INFO] Total running time: 0h0m47s