[2023-03-15 09:48:16,399] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,399] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,399] [INFO] DQC Reference Directory: /var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference
[2023-03-15 09:48:18,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stgcc2182c1-96c1-4e2c-b206-ba8e7f31d70a/OceanDNA-b10502.fa | prodigal -d OceanDNA-b10502/cds.fna -a OceanDNA-b10502/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:27,589] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:27,589] [INFO] Task started: HMMsearch
[2023-03-15 09:48:27,589] [INFO] Running command: hmmsearch --tblout OceanDNA-b10502/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference/reference_markers.hmm OceanDNA-b10502/protein.faa > /dev/null
[2023-03-15 09:48:27,779] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:27,780] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcc2182c1-96c1-4e2c-b206-ba8e7f31d70a/OceanDNA-b10502.fa]
[2023-03-15 09:48:27,790] [INFO] Query marker FASTA was written to OceanDNA-b10502/markers.fasta
[2023-03-15 09:48:27,791] [INFO] Task started: Blastn
[2023-03-15 09:48:27,791] [INFO] Running command: blastn -query OceanDNA-b10502/markers.fasta -db /var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference/reference_markers.fasta -out OceanDNA-b10502/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:28,327] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:28,327] [INFO] Selected 17 target genomes.
[2023-03-15 09:48:28,328] [INFO] Target genome list was writen to OceanDNA-b10502/target_genomes.txt
[2023-03-15 09:48:28,364] [INFO] Task started: fastANI
[2023-03-15 09:48:28,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc2182c1-96c1-4e2c-b206-ba8e7f31d70a/OceanDNA-b10502.fa --refList OceanDNA-b10502/target_genomes.txt --output OceanDNA-b10502/fastani_result.tsv --threads 1
[2023-03-15 09:48:39,212] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:39,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:39,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:39,213] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:39,213] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:39,213] [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
--------------------------------------------------------------------------------
[2023-03-15 09:48:39,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10502/tc_result.tsv
[2023-03-15 09:48:39,213] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:39,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:39,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference/checkm_data
[2023-03-15 09:48:39,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:39,219] [INFO] Task started: CheckM
[2023-03-15 09:48:39,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10502/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10502/checkm_input OceanDNA-b10502/checkm_result
[2023-03-15 09:49:08,175] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:08,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:08,178] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:08,178] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:08,178] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10502/markers.fasta)
[2023-03-15 09:49:08,178] [INFO] Task started: Blastn
[2023-03-15 09:49:08,178] [INFO] Running command: blastn -query OceanDNA-b10502/markers.fasta -db /var/lib/cwl/stgf190c8af-c3a5-4707-a71e-e42a4eab24d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10502/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:08,900] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:08,901] [INFO] Selected 17 target genomes.
[2023-03-15 09:49:08,901] [INFO] Target genome list was writen to OceanDNA-b10502/target_genomes_gtdb.txt
[2023-03-15 09:49:09,100] [INFO] Task started: fastANI
[2023-03-15 09:49:09,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc2182c1-96c1-4e2c-b206-ba8e7f31d70a/OceanDNA-b10502.fa --refList OceanDNA-b10502/target_genomes_gtdb.txt --output OceanDNA-b10502/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:18,989] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:18,992] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:18,992] [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_016780435.1	s__UBA3478 sp016780435	78.0591	62	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3478	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402205.1	s__UBA3478 sp018402205	77.6266	119	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3478	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:18,992] [INFO] GTDB search result was written to OceanDNA-b10502/result_gtdb.tsv
[2023-03-15 09:49:18,992] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:18,993] [INFO] DFAST_QC result json was written to OceanDNA-b10502/dqc_result.json
[2023-03-15 09:49:18,993] [INFO] DFAST_QC completed!
[2023-03-15 09:49:18,993] [INFO] Total running time: 0h1m3s