[2023-03-18 23:44:06,275] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,276] [INFO] DQC Reference Directory: /var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference
[2023-03-18 23:44:07,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,411] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,411] [INFO] Running command: cat /var/lib/cwl/stg975e6d18-4ac1-4794-8a97-c6d303e745ff/OceanDNA-b11647.fa | prodigal -d OceanDNA-b11647/cds.fna -a OceanDNA-b11647/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:23,213] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:23,213] [INFO] Task started: HMMsearch
[2023-03-18 23:44:23,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b11647/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference/reference_markers.hmm OceanDNA-b11647/protein.faa > /dev/null
[2023-03-18 23:44:23,414] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:23,415] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg975e6d18-4ac1-4794-8a97-c6d303e745ff/OceanDNA-b11647.fa]
[2023-03-18 23:44:23,432] [INFO] Query marker FASTA was written to OceanDNA-b11647/markers.fasta
[2023-03-18 23:44:23,432] [INFO] Task started: Blastn
[2023-03-18 23:44:23,432] [INFO] Running command: blastn -query OceanDNA-b11647/markers.fasta -db /var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference/reference_markers.fasta -out OceanDNA-b11647/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:23,956] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:23,956] [INFO] Selected 19 target genomes.
[2023-03-18 23:44:23,957] [INFO] Target genome list was writen to OceanDNA-b11647/target_genomes.txt
[2023-03-18 23:44:23,973] [INFO] Task started: fastANI
[2023-03-18 23:44:23,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg975e6d18-4ac1-4794-8a97-c6d303e745ff/OceanDNA-b11647.fa --refList OceanDNA-b11647/target_genomes.txt --output OceanDNA-b11647/fastani_result.tsv --threads 1
[2023-03-18 23:44:33,907] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:33,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:33,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:33,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:33,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:44:33,908] [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 23:44:33,909] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11647/tc_result.tsv
[2023-03-18 23:44:33,909] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:33,909] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:33,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference/checkm_data
[2023-03-18 23:44:33,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:33,922] [INFO] Task started: CheckM
[2023-03-18 23:44:33,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11647/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11647/checkm_input OceanDNA-b11647/checkm_result
[2023-03-18 23:45:16,445] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:16,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:16,448] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:16,448] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:16,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11647/markers.fasta)
[2023-03-18 23:45:16,450] [INFO] Task started: Blastn
[2023-03-18 23:45:16,450] [INFO] Running command: blastn -query OceanDNA-b11647/markers.fasta -db /var/lib/cwl/stga472048c-1058-4e60-a904-3562fbf54525/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11647/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:17,183] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:17,184] [INFO] Selected 15 target genomes.
[2023-03-18 23:45:17,184] [INFO] Target genome list was writen to OceanDNA-b11647/target_genomes_gtdb.txt
[2023-03-18 23:45:17,196] [INFO] Task started: fastANI
[2023-03-18 23:45:17,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg975e6d18-4ac1-4794-8a97-c6d303e745ff/OceanDNA-b11647.fa --refList OceanDNA-b11647/target_genomes_gtdb.txt --output OceanDNA-b11647/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:25,389] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:25,392] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:45:25,392] [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_000981645.1	s__ASP10-05a sp000981645	99.3991	789	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__ASP10-05a	95.0	99.43	99.38	0.95	0.94	4	conclusive
GCA_905182895.1	s__ASP10-05a sp905182895	91.6368	425	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__ASP10-05a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336675.1	s__ASP10-05a sp002336675	90.5247	613	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__ASP10-05a	95.0	99.85	99.85	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:25,392] [INFO] GTDB search result was written to OceanDNA-b11647/result_gtdb.tsv
[2023-03-18 23:45:25,392] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:25,393] [INFO] DFAST_QC result json was written to OceanDNA-b11647/dqc_result.json
[2023-03-18 23:45:25,393] [INFO] DFAST_QC completed!
[2023-03-18 23:45:25,393] [INFO] Total running time: 0h1m19s