[2023-03-18 00:13:25,300] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:13:25,300] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:13:25,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference
[2023-03-18 00:13:26,442] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:13:26,443] [INFO] Task started: Prodigal
[2023-03-18 00:13:26,443] [INFO] Running command: cat /var/lib/cwl/stg367cf867-0720-4833-8e3b-05f44f0cfe78/OceanDNA-b3902.fa | prodigal -d OceanDNA-b3902/cds.fna -a OceanDNA-b3902/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:13:46,144] [INFO] Task succeeded: Prodigal
[2023-03-18 00:13:46,144] [INFO] Task started: HMMsearch
[2023-03-18 00:13:46,144] [INFO] Running command: hmmsearch --tblout OceanDNA-b3902/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference/reference_markers.hmm OceanDNA-b3902/protein.faa > /dev/null
[2023-03-18 00:13:46,366] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:13:46,366] [INFO] Found 6/6 markers.
[2023-03-18 00:13:46,392] [INFO] Query marker FASTA was written to OceanDNA-b3902/markers.fasta
[2023-03-18 00:13:46,393] [INFO] Task started: Blastn
[2023-03-18 00:13:46,393] [INFO] Running command: blastn -query OceanDNA-b3902/markers.fasta -db /var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference/reference_markers.fasta -out OceanDNA-b3902/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:13:46,909] [INFO] Task succeeded: Blastn
[2023-03-18 00:13:46,910] [INFO] Selected 28 target genomes.
[2023-03-18 00:13:46,910] [INFO] Target genome list was writen to OceanDNA-b3902/target_genomes.txt
[2023-03-18 00:13:46,924] [INFO] Task started: fastANI
[2023-03-18 00:13:46,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg367cf867-0720-4833-8e3b-05f44f0cfe78/OceanDNA-b3902.fa --refList OceanDNA-b3902/target_genomes.txt --output OceanDNA-b3902/fastani_result.tsv --threads 1
[2023-03-18 00:14:04,628] [INFO] Task succeeded: fastANI
[2023-03-18 00:14:04,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:14:04,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:14:04,632] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:14:04,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:14:04,632] [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
Bernardetia litoralis	strain=DSM 6794	GCA_000265505.1	999	999	type	True	79.8998	582	862	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:14:04,632] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3902/tc_result.tsv
[2023-03-18 00:14:04,633] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:14:04,633] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:14:04,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference/checkm_data
[2023-03-18 00:14:04,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:14:04,701] [INFO] Task started: CheckM
[2023-03-18 00:14:04,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3902/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3902/checkm_input OceanDNA-b3902/checkm_result
[2023-03-18 00:14:56,942] [INFO] Task succeeded: CheckM
[2023-03-18 00:14:56,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.76%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:14:56,952] [INFO] ===== Completeness check finished =====
[2023-03-18 00:14:56,952] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:14:56,952] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3902/markers.fasta)
[2023-03-18 00:14:56,954] [INFO] Task started: Blastn
[2023-03-18 00:14:56,954] [INFO] Running command: blastn -query OceanDNA-b3902/markers.fasta -db /var/lib/cwl/stg4a6c3808-b0c4-4bb9-8c64-9819d10d9db7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3902/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:14:57,655] [INFO] Task succeeded: Blastn
[2023-03-18 00:14:57,658] [INFO] Selected 26 target genomes.
[2023-03-18 00:14:57,658] [INFO] Target genome list was writen to OceanDNA-b3902/target_genomes_gtdb.txt
[2023-03-18 00:14:57,684] [INFO] Task started: fastANI
[2023-03-18 00:14:57,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg367cf867-0720-4833-8e3b-05f44f0cfe78/OceanDNA-b3902.fa --refList OceanDNA-b3902/target_genomes_gtdb.txt --output OceanDNA-b3902/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:15:14,185] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:14,188] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:15:14,188] [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_002784125.1	s__Bernardetia sp002784125	80.4889	535	862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Bernardetiaceae;g__Bernardetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265505.1	s__Bernardetia litoralis	79.9186	580	862	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Bernardetiaceae;g__Bernardetia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:15:14,189] [INFO] GTDB search result was written to OceanDNA-b3902/result_gtdb.tsv
[2023-03-18 00:15:14,190] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:15:14,191] [INFO] DFAST_QC result json was written to OceanDNA-b3902/dqc_result.json
[2023-03-18 00:15:14,191] [INFO] DFAST_QC completed!
[2023-03-18 00:15:14,191] [INFO] Total running time: 0h1m49s