[2023-03-16 10:57:32,758] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:57:32,759] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:57:32,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference
[2023-03-16 10:57:33,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:57:33,888] [INFO] Task started: Prodigal
[2023-03-16 10:57:33,888] [INFO] Running command: cat /var/lib/cwl/stg14803b0a-590b-44cf-a951-1eb312c0a37b/OceanDNA-b15327.fa | prodigal -d OceanDNA-b15327/cds.fna -a OceanDNA-b15327/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:57:39,193] [INFO] Task succeeded: Prodigal
[2023-03-16 10:57:39,193] [INFO] Task started: HMMsearch
[2023-03-16 10:57:39,193] [INFO] Running command: hmmsearch --tblout OceanDNA-b15327/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference/reference_markers.hmm OceanDNA-b15327/protein.faa > /dev/null
[2023-03-16 10:57:39,341] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:57:39,342] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg14803b0a-590b-44cf-a951-1eb312c0a37b/OceanDNA-b15327.fa]
[2023-03-16 10:57:39,350] [INFO] Query marker FASTA was written to OceanDNA-b15327/markers.fasta
[2023-03-16 10:57:39,352] [INFO] Task started: Blastn
[2023-03-16 10:57:39,352] [INFO] Running command: blastn -query OceanDNA-b15327/markers.fasta -db /var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference/reference_markers.fasta -out OceanDNA-b15327/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:57:39,874] [INFO] Task succeeded: Blastn
[2023-03-16 10:57:39,875] [INFO] Selected 12 target genomes.
[2023-03-16 10:57:39,875] [INFO] Target genome list was writen to OceanDNA-b15327/target_genomes.txt
[2023-03-16 10:57:39,882] [INFO] Task started: fastANI
[2023-03-16 10:57:39,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg14803b0a-590b-44cf-a951-1eb312c0a37b/OceanDNA-b15327.fa --refList OceanDNA-b15327/target_genomes.txt --output OceanDNA-b15327/fastani_result.tsv --threads 1
[2023-03-16 10:57:45,358] [INFO] Task succeeded: fastANI
[2023-03-16 10:57:45,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:57:45,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:57:45,359] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:57:45,359] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:57:45,359] [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 10:57:45,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15327/tc_result.tsv
[2023-03-16 10:57:45,359] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:57:45,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:57:45,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference/checkm_data
[2023-03-16 10:57:45,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:57:45,372] [INFO] Task started: CheckM
[2023-03-16 10:57:45,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15327/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15327/checkm_input OceanDNA-b15327/checkm_result
[2023-03-16 10:58:05,068] [INFO] Task succeeded: CheckM
[2023-03-16 10:58:05,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.38%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:58:05,070] [INFO] ===== Completeness check finished =====
[2023-03-16 10:58:05,070] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:58:05,070] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15327/markers.fasta)
[2023-03-16 10:58:05,071] [INFO] Task started: Blastn
[2023-03-16 10:58:05,071] [INFO] Running command: blastn -query OceanDNA-b15327/markers.fasta -db /var/lib/cwl/stg5bcc34af-3ee2-40bd-b05a-f7146df353c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15327/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:58:05,829] [INFO] Task succeeded: Blastn
[2023-03-16 10:58:05,830] [INFO] Selected 18 target genomes.
[2023-03-16 10:58:05,830] [INFO] Target genome list was writen to OceanDNA-b15327/target_genomes_gtdb.txt
[2023-03-16 10:58:05,947] [INFO] Task started: fastANI
[2023-03-16 10:58:05,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg14803b0a-590b-44cf-a951-1eb312c0a37b/OceanDNA-b15327.fa --refList OceanDNA-b15327/target_genomes_gtdb.txt --output OceanDNA-b15327/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:58:12,440] [INFO] Task succeeded: fastANI
[2023-03-16 10:58:12,442] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:58:12,442] [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_002712585.1	s__GCA-2712585 sp002712585	81.6295	191	314	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__GCA-2712585;g__GCA-2712585	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:58:12,442] [INFO] GTDB search result was written to OceanDNA-b15327/result_gtdb.tsv
[2023-03-16 10:58:12,443] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:58:12,443] [INFO] DFAST_QC result json was written to OceanDNA-b15327/dqc_result.json
[2023-03-16 10:58:12,443] [INFO] DFAST_QC completed!
[2023-03-16 10:58:12,443] [INFO] Total running time: 0h0m40s