[2023-03-16 21:29:26,236] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:29:26,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:29:26,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference
[2023-03-16 21:29:28,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:29:28,573] [INFO] Task started: Prodigal
[2023-03-16 21:29:28,573] [INFO] Running command: cat /var/lib/cwl/stg96d38ce1-2684-4579-b189-4a43c7635e8a/OceanDNA-b46646.fa | prodigal -d OceanDNA-b46646/cds.fna -a OceanDNA-b46646/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:30:15,315] [INFO] Task succeeded: Prodigal
[2023-03-16 21:30:15,315] [INFO] Task started: HMMsearch
[2023-03-16 21:30:15,315] [INFO] Running command: hmmsearch --tblout OceanDNA-b46646/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference/reference_markers.hmm OceanDNA-b46646/protein.faa > /dev/null
[2023-03-16 21:30:15,582] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:30:15,583] [INFO] Found 6/6 markers.
[2023-03-16 21:30:15,612] [INFO] Query marker FASTA was written to OceanDNA-b46646/markers.fasta
[2023-03-16 21:30:15,612] [INFO] Task started: Blastn
[2023-03-16 21:30:15,612] [INFO] Running command: blastn -query OceanDNA-b46646/markers.fasta -db /var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference/reference_markers.fasta -out OceanDNA-b46646/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:30:16,512] [INFO] Task succeeded: Blastn
[2023-03-16 21:30:16,513] [INFO] Selected 26 target genomes.
[2023-03-16 21:30:16,514] [INFO] Target genome list was writen to OceanDNA-b46646/target_genomes.txt
[2023-03-16 21:30:16,528] [INFO] Task started: fastANI
[2023-03-16 21:30:16,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d38ce1-2684-4579-b189-4a43c7635e8a/OceanDNA-b46646.fa --refList OceanDNA-b46646/target_genomes.txt --output OceanDNA-b46646/fastani_result.tsv --threads 1
[2023-03-16 21:30:33,846] [INFO] Task succeeded: fastANI
[2023-03-16 21:30:33,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:30:33,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:30:33,847] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:30:33,847] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:30:33,847] [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 21:30:34,022] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46646/tc_result.tsv
[2023-03-16 21:30:34,023] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:30:34,023] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:30:34,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference/checkm_data
[2023-03-16 21:30:34,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:30:34,116] [INFO] Task started: CheckM
[2023-03-16 21:30:34,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46646/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46646/checkm_input OceanDNA-b46646/checkm_result
[2023-03-16 21:32:18,965] [INFO] Task succeeded: CheckM
[2023-03-16 21:32:18,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:32:18,969] [INFO] ===== Completeness check finished =====
[2023-03-16 21:32:18,969] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:32:18,970] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46646/markers.fasta)
[2023-03-16 21:32:18,971] [INFO] Task started: Blastn
[2023-03-16 21:32:18,971] [INFO] Running command: blastn -query OceanDNA-b46646/markers.fasta -db /var/lib/cwl/stg368fe97a-12e7-464b-bedf-b4f272ce6dfa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46646/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:32:20,058] [INFO] Task succeeded: Blastn
[2023-03-16 21:32:20,059] [INFO] Selected 31 target genomes.
[2023-03-16 21:32:20,059] [INFO] Target genome list was writen to OceanDNA-b46646/target_genomes_gtdb.txt
[2023-03-16 21:32:20,627] [INFO] Task started: fastANI
[2023-03-16 21:32:20,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d38ce1-2684-4579-b189-4a43c7635e8a/OceanDNA-b46646.fa --refList OceanDNA-b46646/target_genomes_gtdb.txt --output OceanDNA-b46646/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:32:56,696] [INFO] Task succeeded: fastANI
[2023-03-16 21:32:56,698] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:32:56,698] [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_016209525.1	s__VHCZ01 sp016209525	75.8417	55	1136	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIBE01;g__VHCZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871535.1	s__VHCZ01 sp016871535	75.7378	56	1136	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIBE01;g__VHCZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:32:56,698] [INFO] GTDB search result was written to OceanDNA-b46646/result_gtdb.tsv
[2023-03-16 21:32:56,699] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:32:56,699] [INFO] DFAST_QC result json was written to OceanDNA-b46646/dqc_result.json
[2023-03-16 21:32:56,699] [INFO] DFAST_QC completed!
[2023-03-16 21:32:56,699] [INFO] Total running time: 0h3m30s