[2023-03-17 02:42:35,483] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:42:35,483] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:42:35,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference
[2023-03-17 02:42:37,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:42:37,681] [INFO] Task started: Prodigal
[2023-03-17 02:42:37,681] [INFO] Running command: cat /var/lib/cwl/stgf00ce16d-9115-4224-acf3-0cc7b66e51f8/OceanDNA-b33606.fa | prodigal -d OceanDNA-b33606/cds.fna -a OceanDNA-b33606/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:42:43,070] [INFO] Task succeeded: Prodigal
[2023-03-17 02:42:43,070] [INFO] Task started: HMMsearch
[2023-03-17 02:42:43,070] [INFO] Running command: hmmsearch --tblout OceanDNA-b33606/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference/reference_markers.hmm OceanDNA-b33606/protein.faa > /dev/null
[2023-03-17 02:42:43,250] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:42:43,251] [INFO] Found 6/6 markers.
[2023-03-17 02:42:43,261] [INFO] Query marker FASTA was written to OceanDNA-b33606/markers.fasta
[2023-03-17 02:42:43,261] [INFO] Task started: Blastn
[2023-03-17 02:42:43,261] [INFO] Running command: blastn -query OceanDNA-b33606/markers.fasta -db /var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference/reference_markers.fasta -out OceanDNA-b33606/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:42:45,017] [INFO] Task succeeded: Blastn
[2023-03-17 02:42:45,018] [INFO] Selected 28 target genomes.
[2023-03-17 02:42:45,018] [INFO] Target genome list was writen to OceanDNA-b33606/target_genomes.txt
[2023-03-17 02:42:45,166] [INFO] Task started: fastANI
[2023-03-17 02:42:45,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgf00ce16d-9115-4224-acf3-0cc7b66e51f8/OceanDNA-b33606.fa --refList OceanDNA-b33606/target_genomes.txt --output OceanDNA-b33606/fastani_result.tsv --threads 1
[2023-03-17 02:43:04,103] [INFO] Task succeeded: fastANI
[2023-03-17 02:43:04,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:43:04,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:43:04,104] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:43:04,104] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:43:04,104] [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
--------------------------------------------------------------------------------
[2023-03-17 02:43:04,104] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33606/tc_result.tsv
[2023-03-17 02:43:04,104] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:43:04,104] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:43:04,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference/checkm_data
[2023-03-17 02:43:04,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:43:04,111] [INFO] Task started: CheckM
[2023-03-17 02:43:04,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33606/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33606/checkm_input OceanDNA-b33606/checkm_result
[2023-03-17 02:43:23,691] [INFO] Task succeeded: CheckM
[2023-03-17 02:43:23,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:43:23,719] [INFO] ===== Completeness check finished =====
[2023-03-17 02:43:23,719] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:43:23,720] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33606/markers.fasta)
[2023-03-17 02:43:23,721] [INFO] Task started: Blastn
[2023-03-17 02:43:23,721] [INFO] Running command: blastn -query OceanDNA-b33606/markers.fasta -db /var/lib/cwl/stg4de174dd-671f-465f-accb-41f4ee4eca5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33606/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:43:24,470] [INFO] Task succeeded: Blastn
[2023-03-17 02:43:24,471] [INFO] Selected 27 target genomes.
[2023-03-17 02:43:24,472] [INFO] Target genome list was writen to OceanDNA-b33606/target_genomes_gtdb.txt
[2023-03-17 02:43:24,628] [INFO] Task started: fastANI
[2023-03-17 02:43:24,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgf00ce16d-9115-4224-acf3-0cc7b66e51f8/OceanDNA-b33606.fa --refList OceanDNA-b33606/target_genomes_gtdb.txt --output OceanDNA-b33606/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:43:38,634] [INFO] Task succeeded: fastANI
[2023-03-17 02:43:38,638] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:43:38,638] [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_002293155.1	s__UBA954 sp002293155	98.2335	264	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	98.25	97.64	0.86	0.78	18	conclusive
GCA_018882795.1	s__UBA954 sp018882795	77.0371	62	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882785.1	s__UBA954 sp018882785	76.9698	62	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970545.1	s__UBA954 sp018970545	76.8269	61	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:43:38,643] [INFO] GTDB search result was written to OceanDNA-b33606/result_gtdb.tsv
[2023-03-17 02:43:38,647] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:43:38,648] [INFO] DFAST_QC result json was written to OceanDNA-b33606/dqc_result.json
[2023-03-17 02:43:38,648] [INFO] DFAST_QC completed!
[2023-03-17 02:43:38,648] [INFO] Total running time: 0h1m3s