[2023-03-16 19:56:08,722] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:56:08,722] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:56:08,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference
[2023-03-16 19:56:09,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:56:09,831] [INFO] Task started: Prodigal
[2023-03-16 19:56:09,831] [INFO] Running command: cat /var/lib/cwl/stg4924937d-71b0-4268-87d9-d43cb622c6e9/OceanDNA-b33133.fa | prodigal -d OceanDNA-b33133/cds.fna -a OceanDNA-b33133/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:56:25,638] [INFO] Task succeeded: Prodigal
[2023-03-16 19:56:25,639] [INFO] Task started: HMMsearch
[2023-03-16 19:56:25,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b33133/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference/reference_markers.hmm OceanDNA-b33133/protein.faa > /dev/null
[2023-03-16 19:56:25,826] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:56:25,826] [INFO] Found 6/6 markers.
[2023-03-16 19:56:25,847] [INFO] Query marker FASTA was written to OceanDNA-b33133/markers.fasta
[2023-03-16 19:56:25,849] [INFO] Task started: Blastn
[2023-03-16 19:56:25,849] [INFO] Running command: blastn -query OceanDNA-b33133/markers.fasta -db /var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference/reference_markers.fasta -out OceanDNA-b33133/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:56:26,444] [INFO] Task succeeded: Blastn
[2023-03-16 19:56:26,445] [INFO] Selected 34 target genomes.
[2023-03-16 19:56:26,445] [INFO] Target genome list was writen to OceanDNA-b33133/target_genomes.txt
[2023-03-16 19:56:26,464] [INFO] Task started: fastANI
[2023-03-16 19:56:26,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg4924937d-71b0-4268-87d9-d43cb622c6e9/OceanDNA-b33133.fa --refList OceanDNA-b33133/target_genomes.txt --output OceanDNA-b33133/fastani_result.tsv --threads 1
[2023-03-16 19:57:04,466] [INFO] Task succeeded: fastANI
[2023-03-16 19:57:04,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:57:04,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:57:04,466] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:57:04,466] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:57:04,466] [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 19:57:04,467] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33133/tc_result.tsv
[2023-03-16 19:57:04,467] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:57:04,467] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:57:04,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference/checkm_data
[2023-03-16 19:57:04,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:57:04,538] [INFO] Task started: CheckM
[2023-03-16 19:57:04,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33133/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33133/checkm_input OceanDNA-b33133/checkm_result
[2023-03-16 19:57:56,021] [INFO] Task succeeded: CheckM
[2023-03-16 19:57:56,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:57:56,024] [INFO] ===== Completeness check finished =====
[2023-03-16 19:57:56,024] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:57:56,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33133/markers.fasta)
[2023-03-16 19:57:56,025] [INFO] Task started: Blastn
[2023-03-16 19:57:56,026] [INFO] Running command: blastn -query OceanDNA-b33133/markers.fasta -db /var/lib/cwl/stg69169a97-643e-468c-a17a-62dcfc37ec76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33133/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:57:57,180] [INFO] Task succeeded: Blastn
[2023-03-16 19:57:57,181] [INFO] Selected 26 target genomes.
[2023-03-16 19:57:57,181] [INFO] Target genome list was writen to OceanDNA-b33133/target_genomes_gtdb.txt
[2023-03-16 19:57:57,212] [INFO] Task started: fastANI
[2023-03-16 19:57:57,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg4924937d-71b0-4268-87d9-d43cb622c6e9/OceanDNA-b33133.fa --refList OceanDNA-b33133/target_genomes_gtdb.txt --output OceanDNA-b33133/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:58:13,830] [INFO] Task succeeded: fastANI
[2023-03-16 19:58:13,833] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:58:13,833] [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_002722095.1	s__UBA8366 sp002722095	99.9682	842	844	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA8366	95.0	99.86	99.86	0.93	0.93	2	conclusive
GCA_002715005.1	s__GCA-002724395 sp002715005	76.184	60	844	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__GCA-002724395	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724395.1	s__GCA-002724395 sp002724395	75.8317	52	844	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__GCA-002724395	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:58:13,834] [INFO] GTDB search result was written to OceanDNA-b33133/result_gtdb.tsv
[2023-03-16 19:58:13,834] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:58:13,834] [INFO] DFAST_QC result json was written to OceanDNA-b33133/dqc_result.json
[2023-03-16 19:58:13,834] [INFO] DFAST_QC completed!
[2023-03-16 19:58:13,834] [INFO] Total running time: 0h2m5s