[2023-03-16 04:54:07,037] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference
[2023-03-16 04:54:08,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,333] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,333] [INFO] Running command: cat /var/lib/cwl/stg50944953-790e-40f5-a72c-0955dcfe633a/OceanDNA-b2947.fa | prodigal -d OceanDNA-b2947/cds.fna -a OceanDNA-b2947/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:13,243] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:13,243] [INFO] Task started: HMMsearch
[2023-03-16 04:54:13,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b2947/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference/reference_markers.hmm OceanDNA-b2947/protein.faa > /dev/null
[2023-03-16 04:54:13,435] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:13,435] [INFO] Found 6/6 markers.
[2023-03-16 04:54:13,445] [INFO] Query marker FASTA was written to OceanDNA-b2947/markers.fasta
[2023-03-16 04:54:13,445] [INFO] Task started: Blastn
[2023-03-16 04:54:13,445] [INFO] Running command: blastn -query OceanDNA-b2947/markers.fasta -db /var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference/reference_markers.fasta -out OceanDNA-b2947/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:13,964] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:13,965] [INFO] Selected 20 target genomes.
[2023-03-16 04:54:13,965] [INFO] Target genome list was writen to OceanDNA-b2947/target_genomes.txt
[2023-03-16 04:54:13,976] [INFO] Task started: fastANI
[2023-03-16 04:54:13,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg50944953-790e-40f5-a72c-0955dcfe633a/OceanDNA-b2947.fa --refList OceanDNA-b2947/target_genomes.txt --output OceanDNA-b2947/fastani_result.tsv --threads 1
[2023-03-16 04:54:22,945] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:22,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:22,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:22,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:22,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:22,946] [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 04:54:22,946] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2947/tc_result.tsv
[2023-03-16 04:54:22,946] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:22,947] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:22,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference/checkm_data
[2023-03-16 04:54:22,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:22,953] [INFO] Task started: CheckM
[2023-03-16 04:54:22,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2947/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2947/checkm_input OceanDNA-b2947/checkm_result
[2023-03-16 04:54:41,533] [INFO] Task succeeded: CheckM
[2023-03-16 04:54:41,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:54:41,535] [INFO] ===== Completeness check finished =====
[2023-03-16 04:54:41,536] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:54:41,536] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2947/markers.fasta)
[2023-03-16 04:54:41,537] [INFO] Task started: Blastn
[2023-03-16 04:54:41,537] [INFO] Running command: blastn -query OceanDNA-b2947/markers.fasta -db /var/lib/cwl/stg1590eb2d-5f04-4d0a-b138-c5a83d81e70b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2947/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:42,287] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:42,288] [INFO] Selected 19 target genomes.
[2023-03-16 04:54:42,288] [INFO] Target genome list was writen to OceanDNA-b2947/target_genomes_gtdb.txt
[2023-03-16 04:54:42,363] [INFO] Task started: fastANI
[2023-03-16 04:54:42,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg50944953-790e-40f5-a72c-0955dcfe633a/OceanDNA-b2947.fa --refList OceanDNA-b2947/target_genomes_gtdb.txt --output OceanDNA-b2947/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:54:46,480] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:46,484] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:54:46,484] [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_014190035.1	s__ATZT02 sp014190035	79.5737	150	287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463095.1	s__ATZT02 sp016463095	79.2736	131	287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	98.85	98.85	0.89	0.89	2	-
GCA_000428345.2	s__ATZT02 sp000428345	79.2508	104	287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789325.1	s__ATZT02 sp005789325	78.6308	90	287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	96.56	96.56	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:54:46,484] [INFO] GTDB search result was written to OceanDNA-b2947/result_gtdb.tsv
[2023-03-16 04:54:46,485] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:54:46,485] [INFO] DFAST_QC result json was written to OceanDNA-b2947/dqc_result.json
[2023-03-16 04:54:46,485] [INFO] DFAST_QC completed!
[2023-03-16 04:54:46,485] [INFO] Total running time: 0h0m39s