[2023-03-18 03:27:00,936] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference
[2023-03-18 03:27:02,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,636] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,636] [INFO] Running command: cat /var/lib/cwl/stg7cefd0da-b397-4de1-9e67-cc05b5d0b343/OceanDNA-b33591.fa | prodigal -d OceanDNA-b33591/cds.fna -a OceanDNA-b33591/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:09,603] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:09,604] [INFO] Task started: HMMsearch
[2023-03-18 03:27:09,604] [INFO] Running command: hmmsearch --tblout OceanDNA-b33591/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference/reference_markers.hmm OceanDNA-b33591/protein.faa > /dev/null
[2023-03-18 03:27:09,790] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:09,790] [INFO] Found 6/6 markers.
[2023-03-18 03:27:09,801] [INFO] Query marker FASTA was written to OceanDNA-b33591/markers.fasta
[2023-03-18 03:27:09,801] [INFO] Task started: Blastn
[2023-03-18 03:27:09,801] [INFO] Running command: blastn -query OceanDNA-b33591/markers.fasta -db /var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference/reference_markers.fasta -out OceanDNA-b33591/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:10,355] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:10,356] [INFO] Selected 17 target genomes.
[2023-03-18 03:27:10,356] [INFO] Target genome list was writen to OceanDNA-b33591/target_genomes.txt
[2023-03-18 03:27:10,365] [INFO] Task started: fastANI
[2023-03-18 03:27:10,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cefd0da-b397-4de1-9e67-cc05b5d0b343/OceanDNA-b33591.fa --refList OceanDNA-b33591/target_genomes.txt --output OceanDNA-b33591/fastani_result.tsv --threads 1
[2023-03-18 03:27:16,595] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:16,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:16,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:16,596] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:16,596] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:16,596] [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 03:27:16,596] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33591/tc_result.tsv
[2023-03-18 03:27:16,596] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:16,596] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:16,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference/checkm_data
[2023-03-18 03:27:16,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:16,602] [INFO] Task started: CheckM
[2023-03-18 03:27:16,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33591/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33591/checkm_input OceanDNA-b33591/checkm_result
[2023-03-18 03:27:39,226] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:39,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:39,232] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:39,233] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:39,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33591/markers.fasta)
[2023-03-18 03:27:39,233] [INFO] Task started: Blastn
[2023-03-18 03:27:39,233] [INFO] Running command: blastn -query OceanDNA-b33591/markers.fasta -db /var/lib/cwl/stg46233c05-0ea3-45fc-8787-c520afdd1bb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33591/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:40,181] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:40,182] [INFO] Selected 25 target genomes.
[2023-03-18 03:27:40,182] [INFO] Target genome list was writen to OceanDNA-b33591/target_genomes_gtdb.txt
[2023-03-18 03:27:40,210] [INFO] Task started: fastANI
[2023-03-18 03:27:40,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cefd0da-b397-4de1-9e67-cc05b5d0b343/OceanDNA-b33591.fa --refList OceanDNA-b33591/target_genomes_gtdb.txt --output OceanDNA-b33591/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:47,395] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:47,398] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:27:47,398] [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_002167365.1	s__UBA7377 sp002167365	99.314	395	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002170285.1	s__UBA7377 sp002170285	77.5655	141	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	98.55	98.55	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:47,398] [INFO] GTDB search result was written to OceanDNA-b33591/result_gtdb.tsv
[2023-03-18 03:27:47,398] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:47,399] [INFO] DFAST_QC result json was written to OceanDNA-b33591/dqc_result.json
[2023-03-18 03:27:47,399] [INFO] DFAST_QC completed!
[2023-03-18 03:27:47,399] [INFO] Total running time: 0h0m46s