[2023-03-15 22:44:22,206] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,207] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,207] [INFO] DQC Reference Directory: /var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference
[2023-03-15 22:44:23,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,277] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,277] [INFO] Running command: cat /var/lib/cwl/stg9aa9c7ce-4f2d-470f-a204-792bc8bd9bb0/OceanDNA-b41613.fa | prodigal -d OceanDNA-b41613/cds.fna -a OceanDNA-b41613/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:27,424] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:27,425] [INFO] Task started: HMMsearch
[2023-03-15 22:44:27,425] [INFO] Running command: hmmsearch --tblout OceanDNA-b41613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference/reference_markers.hmm OceanDNA-b41613/protein.faa > /dev/null
[2023-03-15 22:44:27,583] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:27,583] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9aa9c7ce-4f2d-470f-a204-792bc8bd9bb0/OceanDNA-b41613.fa]
[2023-03-15 22:44:27,611] [INFO] Query marker FASTA was written to OceanDNA-b41613/markers.fasta
[2023-03-15 22:44:27,612] [INFO] Task started: Blastn
[2023-03-15 22:44:27,612] [INFO] Running command: blastn -query OceanDNA-b41613/markers.fasta -db /var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference/reference_markers.fasta -out OceanDNA-b41613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:28,122] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:28,131] [INFO] Selected 23 target genomes.
[2023-03-15 22:44:28,131] [INFO] Target genome list was writen to OceanDNA-b41613/target_genomes.txt
[2023-03-15 22:44:28,143] [INFO] Task started: fastANI
[2023-03-15 22:44:28,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa9c7ce-4f2d-470f-a204-792bc8bd9bb0/OceanDNA-b41613.fa --refList OceanDNA-b41613/target_genomes.txt --output OceanDNA-b41613/fastani_result.tsv --threads 1
[2023-03-15 22:44:41,287] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:41,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:41,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:41,288] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:41,288] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:44:41,288] [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 22:44:41,292] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41613/tc_result.tsv
[2023-03-15 22:44:41,300] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:41,300] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:41,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference/checkm_data
[2023-03-15 22:44:41,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:41,406] [INFO] Task started: CheckM
[2023-03-15 22:44:41,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41613/checkm_input OceanDNA-b41613/checkm_result
[2023-03-15 22:44:58,450] [INFO] Task succeeded: CheckM
[2023-03-15 22:44:58,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.96%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 22:44:58,634] [INFO] ===== Completeness check finished =====
[2023-03-15 22:44:58,634] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:44:58,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41613/markers.fasta)
[2023-03-15 22:44:58,636] [INFO] Task started: Blastn
[2023-03-15 22:44:58,636] [INFO] Running command: blastn -query OceanDNA-b41613/markers.fasta -db /var/lib/cwl/stge6c6ffbc-8692-4534-9e1a-f2e7648e90dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:59,305] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:59,308] [INFO] Selected 15 target genomes.
[2023-03-15 22:44:59,308] [INFO] Target genome list was writen to OceanDNA-b41613/target_genomes_gtdb.txt
[2023-03-15 22:44:59,378] [INFO] Task started: fastANI
[2023-03-15 22:44:59,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa9c7ce-4f2d-470f-a204-792bc8bd9bb0/OceanDNA-b41613.fa --refList OceanDNA-b41613/target_genomes_gtdb.txt --output OceanDNA-b41613/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:06,161] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:06,164] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:45:06,164] [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_002339085.1	s__UBA7434 sp002339085	91.1552	209	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	-
GCA_002726445.1	s__UBA7434 sp002726445	87.8868	155	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.17	99.17	0.72	0.72	2	-
GCA_002336035.1	s__UBA7434 sp002336035	78.2373	105	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:06,169] [INFO] GTDB search result was written to OceanDNA-b41613/result_gtdb.tsv
[2023-03-15 22:45:06,180] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:06,187] [INFO] DFAST_QC result json was written to OceanDNA-b41613/dqc_result.json
[2023-03-15 22:45:06,187] [INFO] DFAST_QC completed!
[2023-03-15 22:45:06,187] [INFO] Total running time: 0h0m44s