[2023-03-17 05:26:45,808] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference
[2023-03-17 05:26:46,920] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,920] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,920] [INFO] Running command: cat /var/lib/cwl/stgedc949cc-7157-44c1-a0dc-cfae315e76ca/OceanDNA-b44621.fa | prodigal -d OceanDNA-b44621/cds.fna -a OceanDNA-b44621/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:26:57,123] [INFO] Task succeeded: Prodigal
[2023-03-17 05:26:57,124] [INFO] Task started: HMMsearch
[2023-03-17 05:26:57,124] [INFO] Running command: hmmsearch --tblout OceanDNA-b44621/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference/reference_markers.hmm OceanDNA-b44621/protein.faa > /dev/null
[2023-03-17 05:26:57,285] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:26:57,285] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgedc949cc-7157-44c1-a0dc-cfae315e76ca/OceanDNA-b44621.fa]
[2023-03-17 05:26:57,304] [INFO] Query marker FASTA was written to OceanDNA-b44621/markers.fasta
[2023-03-17 05:26:57,304] [INFO] Task started: Blastn
[2023-03-17 05:26:57,304] [INFO] Running command: blastn -query OceanDNA-b44621/markers.fasta -db /var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference/reference_markers.fasta -out OceanDNA-b44621/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:26:57,874] [INFO] Task succeeded: Blastn
[2023-03-17 05:26:57,875] [INFO] Selected 24 target genomes.
[2023-03-17 05:26:57,875] [INFO] Target genome list was writen to OceanDNA-b44621/target_genomes.txt
[2023-03-17 05:26:57,890] [INFO] Task started: fastANI
[2023-03-17 05:26:57,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgedc949cc-7157-44c1-a0dc-cfae315e76ca/OceanDNA-b44621.fa --refList OceanDNA-b44621/target_genomes.txt --output OceanDNA-b44621/fastani_result.tsv --threads 1
[2023-03-17 05:27:12,391] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:12,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:12,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:12,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:27:12,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:27:12,392] [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 05:27:12,392] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44621/tc_result.tsv
[2023-03-17 05:27:12,392] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:12,392] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:12,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference/checkm_data
[2023-03-17 05:27:12,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:12,399] [INFO] Task started: CheckM
[2023-03-17 05:27:12,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44621/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44621/checkm_input OceanDNA-b44621/checkm_result
[2023-03-17 05:27:42,283] [INFO] Task succeeded: CheckM
[2023-03-17 05:27:42,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:27:42,285] [INFO] ===== Completeness check finished =====
[2023-03-17 05:27:42,285] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:27:42,285] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44621/markers.fasta)
[2023-03-17 05:27:42,286] [INFO] Task started: Blastn
[2023-03-17 05:27:42,287] [INFO] Running command: blastn -query OceanDNA-b44621/markers.fasta -db /var/lib/cwl/stg6dd60b3b-709a-4785-aaec-ceea38d30ba5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44621/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:43,113] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:43,113] [INFO] Selected 21 target genomes.
[2023-03-17 05:27:43,114] [INFO] Target genome list was writen to OceanDNA-b44621/target_genomes_gtdb.txt
[2023-03-17 05:27:43,330] [INFO] Task started: fastANI
[2023-03-17 05:27:43,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgedc949cc-7157-44c1-a0dc-cfae315e76ca/OceanDNA-b44621.fa --refList OceanDNA-b44621/target_genomes_gtdb.txt --output OceanDNA-b44621/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:27:55,175] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:55,178] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:27:55,178] [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_013042375.1	s__UBA1847 sp013042375	76.8371	55	471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_009937505.1	s__JAACFE01 sp009937505	76.6302	51	471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937525.1	s__JAACFE01 sp009937525	76.2965	69	471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:27:55,178] [INFO] GTDB search result was written to OceanDNA-b44621/result_gtdb.tsv
[2023-03-17 05:27:55,178] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:27:55,179] [INFO] DFAST_QC result json was written to OceanDNA-b44621/dqc_result.json
[2023-03-17 05:27:55,179] [INFO] DFAST_QC completed!
[2023-03-17 05:27:55,179] [INFO] Total running time: 0h1m9s