[2023-03-17 23:55:11,398] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:55:11,400] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:55:11,400] [INFO] DQC Reference Directory: /var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference
[2023-03-17 23:55:12,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:55:12,534] [INFO] Task started: Prodigal
[2023-03-17 23:55:12,534] [INFO] Running command: cat /var/lib/cwl/stgb44f22eb-a9c0-4db7-b386-cfdd13e1f135/OceanDNA-b45572.fa | prodigal -d OceanDNA-b45572/cds.fna -a OceanDNA-b45572/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:55:24,779] [INFO] Task succeeded: Prodigal
[2023-03-17 23:55:24,779] [INFO] Task started: HMMsearch
[2023-03-17 23:55:24,779] [INFO] Running command: hmmsearch --tblout OceanDNA-b45572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference/reference_markers.hmm OceanDNA-b45572/protein.faa > /dev/null
[2023-03-17 23:55:24,919] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:55:24,919] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb44f22eb-a9c0-4db7-b386-cfdd13e1f135/OceanDNA-b45572.fa]
[2023-03-17 23:55:24,940] [INFO] Query marker FASTA was written to OceanDNA-b45572/markers.fasta
[2023-03-17 23:55:24,942] [INFO] Task started: Blastn
[2023-03-17 23:55:24,942] [INFO] Running command: blastn -query OceanDNA-b45572/markers.fasta -db /var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference/reference_markers.fasta -out OceanDNA-b45572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:55:25,377] [INFO] Task succeeded: Blastn
[2023-03-17 23:55:25,386] [INFO] Selected 4 target genomes.
[2023-03-17 23:55:25,386] [INFO] Target genome list was writen to OceanDNA-b45572/target_genomes.txt
[2023-03-17 23:55:25,389] [INFO] Task started: fastANI
[2023-03-17 23:55:25,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgb44f22eb-a9c0-4db7-b386-cfdd13e1f135/OceanDNA-b45572.fa --refList OceanDNA-b45572/target_genomes.txt --output OceanDNA-b45572/fastani_result.tsv --threads 1
[2023-03-17 23:55:27,603] [INFO] Task succeeded: fastANI
[2023-03-17 23:55:27,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:55:27,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:55:27,604] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:55:27,604] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:55:27,604] [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
--------------------------------------------------------------------------------
[2023-03-17 23:55:27,608] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45572/tc_result.tsv
[2023-03-17 23:55:27,611] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:55:27,611] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:55:27,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference/checkm_data
[2023-03-17 23:55:27,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:55:27,621] [INFO] Task started: CheckM
[2023-03-17 23:55:27,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45572/checkm_input OceanDNA-b45572/checkm_result
[2023-03-17 23:56:03,786] [INFO] Task succeeded: CheckM
[2023-03-17 23:56:03,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.65%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:56:03,806] [INFO] ===== Completeness check finished =====
[2023-03-17 23:56:03,807] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:56:03,807] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45572/markers.fasta)
[2023-03-17 23:56:03,808] [INFO] Task started: Blastn
[2023-03-17 23:56:03,808] [INFO] Running command: blastn -query OceanDNA-b45572/markers.fasta -db /var/lib/cwl/stgafce6096-af53-4352-9264-136eb5b608fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:56:04,250] [INFO] Task succeeded: Blastn
[2023-03-17 23:56:04,259] [INFO] Selected 5 target genomes.
[2023-03-17 23:56:04,259] [INFO] Target genome list was writen to OceanDNA-b45572/target_genomes_gtdb.txt
[2023-03-17 23:56:04,262] [INFO] Task started: fastANI
[2023-03-17 23:56:04,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgb44f22eb-a9c0-4db7-b386-cfdd13e1f135/OceanDNA-b45572.fa --refList OceanDNA-b45572/target_genomes_gtdb.txt --output OceanDNA-b45572/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:56:06,587] [INFO] Task succeeded: fastANI
[2023-03-17 23:56:06,589] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:56:06,589] [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_018645725.1	s__MB11C04 sp018645725	81.8523	81	138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	78.6592	57	138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
--------------------------------------------------------------------------------
[2023-03-17 23:56:06,591] [INFO] GTDB search result was written to OceanDNA-b45572/result_gtdb.tsv
[2023-03-17 23:56:06,595] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:56:06,597] [INFO] DFAST_QC result json was written to OceanDNA-b45572/dqc_result.json
[2023-03-17 23:56:06,598] [INFO] DFAST_QC completed!
[2023-03-17 23:56:06,598] [INFO] Total running time: 0h0m55s