[2023-03-16 04:54:07,042] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference
[2023-03-16 04:54:08,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,331] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,331] [INFO] Running command: cat /var/lib/cwl/stg03b60377-63f7-4cc9-990f-b57c18b5513a/OceanDNA-b13541.fa | prodigal -d OceanDNA-b13541/cds.fna -a OceanDNA-b13541/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:18,330] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:18,331] [INFO] Task started: HMMsearch
[2023-03-16 04:54:18,331] [INFO] Running command: hmmsearch --tblout OceanDNA-b13541/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference/reference_markers.hmm OceanDNA-b13541/protein.faa > /dev/null
[2023-03-16 04:54:18,543] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:18,544] [INFO] Found 6/6 markers.
[2023-03-16 04:54:18,565] [INFO] Query marker FASTA was written to OceanDNA-b13541/markers.fasta
[2023-03-16 04:54:18,565] [INFO] Task started: Blastn
[2023-03-16 04:54:18,565] [INFO] Running command: blastn -query OceanDNA-b13541/markers.fasta -db /var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference/reference_markers.fasta -out OceanDNA-b13541/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:19,131] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:19,131] [INFO] Selected 24 target genomes.
[2023-03-16 04:54:19,132] [INFO] Target genome list was writen to OceanDNA-b13541/target_genomes.txt
[2023-03-16 04:54:19,149] [INFO] Task started: fastANI
[2023-03-16 04:54:19,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg03b60377-63f7-4cc9-990f-b57c18b5513a/OceanDNA-b13541.fa --refList OceanDNA-b13541/target_genomes.txt --output OceanDNA-b13541/fastani_result.tsv --threads 1
[2023-03-16 04:54:36,308] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:36,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:36,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:36,309] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:36,309] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:36,309] [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 04:54:36,310] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13541/tc_result.tsv
[2023-03-16 04:54:36,310] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:36,310] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:36,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference/checkm_data
[2023-03-16 04:54:36,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:36,319] [INFO] Task started: CheckM
[2023-03-16 04:54:36,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13541/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13541/checkm_input OceanDNA-b13541/checkm_result
[2023-03-16 04:55:05,583] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:05,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:05,587] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:05,587] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:05,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13541/markers.fasta)
[2023-03-16 04:55:05,587] [INFO] Task started: Blastn
[2023-03-16 04:55:05,587] [INFO] Running command: blastn -query OceanDNA-b13541/markers.fasta -db /var/lib/cwl/stgfea0b96f-15a2-4e1c-a7a4-2b5462b32d0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13541/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:06,488] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:06,490] [INFO] Selected 23 target genomes.
[2023-03-16 04:55:06,490] [INFO] Target genome list was writen to OceanDNA-b13541/target_genomes_gtdb.txt
[2023-03-16 04:55:06,538] [INFO] Task started: fastANI
[2023-03-16 04:55:06,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg03b60377-63f7-4cc9-990f-b57c18b5513a/OceanDNA-b13541.fa --refList OceanDNA-b13541/target_genomes_gtdb.txt --output OceanDNA-b13541/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:19,327] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:19,329] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:19,330] [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_018648225.1	s__NIOZ-UU35 sp018648225	99.358	276	303	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__NIOZ-UU35	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014382605.1	s__NIOZ-UU35 sp014382605	88.7726	233	303	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__NIOZ-UU35	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:19,330] [INFO] GTDB search result was written to OceanDNA-b13541/result_gtdb.tsv
[2023-03-16 04:55:19,330] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:19,331] [INFO] DFAST_QC result json was written to OceanDNA-b13541/dqc_result.json
[2023-03-16 04:55:19,331] [INFO] DFAST_QC completed!
[2023-03-16 04:55:19,331] [INFO] Total running time: 0h1m12s