[2023-03-18 03:09:35,401] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:35,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:35,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference
[2023-03-18 03:09:36,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:36,636] [INFO] Task started: Prodigal
[2023-03-18 03:09:36,636] [INFO] Running command: cat /var/lib/cwl/stg5d751fe1-d66f-4070-9c80-1418e476526b/OceanDNA-b17084.fa | prodigal -d OceanDNA-b17084/cds.fna -a OceanDNA-b17084/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:43,692] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:43,692] [INFO] Task started: HMMsearch
[2023-03-18 03:09:43,693] [INFO] Running command: hmmsearch --tblout OceanDNA-b17084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference/reference_markers.hmm OceanDNA-b17084/protein.faa > /dev/null
[2023-03-18 03:09:43,917] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:43,917] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d751fe1-d66f-4070-9c80-1418e476526b/OceanDNA-b17084.fa]
[2023-03-18 03:09:43,932] [INFO] Query marker FASTA was written to OceanDNA-b17084/markers.fasta
[2023-03-18 03:09:43,932] [INFO] Task started: Blastn
[2023-03-18 03:09:43,932] [INFO] Running command: blastn -query OceanDNA-b17084/markers.fasta -db /var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference/reference_markers.fasta -out OceanDNA-b17084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:44,458] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:44,459] [INFO] Selected 31 target genomes.
[2023-03-18 03:09:44,459] [INFO] Target genome list was writen to OceanDNA-b17084/target_genomes.txt
[2023-03-18 03:09:44,477] [INFO] Task started: fastANI
[2023-03-18 03:09:44,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d751fe1-d66f-4070-9c80-1418e476526b/OceanDNA-b17084.fa --refList OceanDNA-b17084/target_genomes.txt --output OceanDNA-b17084/fastani_result.tsv --threads 1
[2023-03-18 03:10:08,787] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:08,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:08,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:08,787] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:08,787] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:10:08,788] [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 03:10:08,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17084/tc_result.tsv
[2023-03-18 03:10:08,788] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:08,788] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:08,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference/checkm_data
[2023-03-18 03:10:08,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:08,794] [INFO] Task started: CheckM
[2023-03-18 03:10:08,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17084/checkm_input OceanDNA-b17084/checkm_result
[2023-03-18 03:10:32,188] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:32,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.48%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:32,190] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:32,191] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:32,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17084/markers.fasta)
[2023-03-18 03:10:32,191] [INFO] Task started: Blastn
[2023-03-18 03:10:32,191] [INFO] Running command: blastn -query OceanDNA-b17084/markers.fasta -db /var/lib/cwl/stg7fd4a2a6-62b6-4892-9faf-eb4698031af6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:32,951] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:32,952] [INFO] Selected 25 target genomes.
[2023-03-18 03:10:32,953] [INFO] Target genome list was writen to OceanDNA-b17084/target_genomes_gtdb.txt
[2023-03-18 03:10:33,052] [INFO] Task started: fastANI
[2023-03-18 03:10:33,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d751fe1-d66f-4070-9c80-1418e476526b/OceanDNA-b17084.fa --refList OceanDNA-b17084/target_genomes_gtdb.txt --output OceanDNA-b17084/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:49,634] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:49,637] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:10:49,637] [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_003597945.1	s__SURF-33 sp003597945	96.3399	242	297	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-33	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011390465.1	s__SURF-3 sp011390465	76.6546	53	297	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:49,638] [INFO] GTDB search result was written to OceanDNA-b17084/result_gtdb.tsv
[2023-03-18 03:10:49,638] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:49,638] [INFO] DFAST_QC result json was written to OceanDNA-b17084/dqc_result.json
[2023-03-18 03:10:49,638] [INFO] DFAST_QC completed!
[2023-03-18 03:10:49,638] [INFO] Total running time: 0h1m14s