[2023-03-15 18:39:12,271] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,272] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg890a2f9b-c03c-47e5-8074-03cab9ec619b/OceanDNA-b24073.fa | prodigal -d OceanDNA-b24073/cds.fna -a OceanDNA-b24073/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:23,701] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:23,701] [INFO] Task started: HMMsearch
[2023-03-15 18:39:23,701] [INFO] Running command: hmmsearch --tblout OceanDNA-b24073/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference/reference_markers.hmm OceanDNA-b24073/protein.faa > /dev/null
[2023-03-15 18:39:23,865] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:23,866] [INFO] Found 6/6 markers.
[2023-03-15 18:39:23,882] [INFO] Query marker FASTA was written to OceanDNA-b24073/markers.fasta
[2023-03-15 18:39:23,882] [INFO] Task started: Blastn
[2023-03-15 18:39:23,882] [INFO] Running command: blastn -query OceanDNA-b24073/markers.fasta -db /var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference/reference_markers.fasta -out OceanDNA-b24073/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:24,460] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:24,460] [INFO] Selected 26 target genomes.
[2023-03-15 18:39:24,461] [INFO] Target genome list was writen to OceanDNA-b24073/target_genomes.txt
[2023-03-15 18:39:24,478] [INFO] Task started: fastANI
[2023-03-15 18:39:24,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg890a2f9b-c03c-47e5-8074-03cab9ec619b/OceanDNA-b24073.fa --refList OceanDNA-b24073/target_genomes.txt --output OceanDNA-b24073/fastani_result.tsv --threads 1
[2023-03-15 18:39:38,858] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:38,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:38,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:38,859] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:38,859] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:38,859] [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
--------------------------------------------------------------------------------
[2023-03-15 18:39:38,859] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24073/tc_result.tsv
[2023-03-15 18:39:38,860] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:38,860] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:38,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference/checkm_data
[2023-03-15 18:39:38,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:38,865] [INFO] Task started: CheckM
[2023-03-15 18:39:38,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24073/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24073/checkm_input OceanDNA-b24073/checkm_result
[2023-03-15 18:40:08,449] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:08,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:08,451] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:08,451] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:08,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24073/markers.fasta)
[2023-03-15 18:40:08,451] [INFO] Task started: Blastn
[2023-03-15 18:40:08,451] [INFO] Running command: blastn -query OceanDNA-b24073/markers.fasta -db /var/lib/cwl/stg5d2a8813-9255-4566-b2d0-75c9aee3f947/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24073/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:09,402] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:09,403] [INFO] Selected 28 target genomes.
[2023-03-15 18:40:09,403] [INFO] Target genome list was writen to OceanDNA-b24073/target_genomes_gtdb.txt
[2023-03-15 18:40:10,058] [INFO] Task started: fastANI
[2023-03-15 18:40:10,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg890a2f9b-c03c-47e5-8074-03cab9ec619b/OceanDNA-b24073.fa --refList OceanDNA-b24073/target_genomes_gtdb.txt --output OceanDNA-b24073/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:23,711] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:23,715] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:40:23,715] [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_905182615.1	s__WLWZ01 sp905182615	98.8481	420	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WLWZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012103315.1	s__WLWZ01 sp012103315	79.3074	375	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WLWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720855.1	s__GCA-2720855 sp002720855	76.6365	125	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__GCA-2720855	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:23,715] [INFO] GTDB search result was written to OceanDNA-b24073/result_gtdb.tsv
[2023-03-15 18:40:23,715] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:23,716] [INFO] DFAST_QC result json was written to OceanDNA-b24073/dqc_result.json
[2023-03-15 18:40:23,716] [INFO] DFAST_QC completed!
[2023-03-15 18:40:23,716] [INFO] Total running time: 0h1m11s