[2023-03-15 20:34:26,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference
[2023-03-15 20:34:28,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,465] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,466] [INFO] Running command: cat /var/lib/cwl/stge5c60eba-613a-4eac-ba50-74f0419daf48/OceanDNA-b38741.fa | prodigal -d OceanDNA-b38741/cds.fna -a OceanDNA-b38741/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:39,669] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:39,669] [INFO] Task started: HMMsearch
[2023-03-15 20:34:39,669] [INFO] Running command: hmmsearch --tblout OceanDNA-b38741/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference/reference_markers.hmm OceanDNA-b38741/protein.faa > /dev/null
[2023-03-15 20:34:39,845] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:39,845] [INFO] Found 6/6 markers.
[2023-03-15 20:34:39,861] [INFO] Query marker FASTA was written to OceanDNA-b38741/markers.fasta
[2023-03-15 20:34:39,861] [INFO] Task started: Blastn
[2023-03-15 20:34:39,861] [INFO] Running command: blastn -query OceanDNA-b38741/markers.fasta -db /var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference/reference_markers.fasta -out OceanDNA-b38741/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:40,398] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:40,399] [INFO] Selected 36 target genomes.
[2023-03-15 20:34:40,399] [INFO] Target genome list was writen to OceanDNA-b38741/target_genomes.txt
[2023-03-15 20:34:40,417] [INFO] Task started: fastANI
[2023-03-15 20:34:40,418] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c60eba-613a-4eac-ba50-74f0419daf48/OceanDNA-b38741.fa --refList OceanDNA-b38741/target_genomes.txt --output OceanDNA-b38741/fastani_result.tsv --threads 1
[2023-03-15 20:35:03,300] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:03,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:03,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:03,301] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:03,301] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:35:03,301] [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 20:35:03,301] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38741/tc_result.tsv
[2023-03-15 20:35:03,301] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:03,301] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:03,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference/checkm_data
[2023-03-15 20:35:03,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:03,308] [INFO] Task started: CheckM
[2023-03-15 20:35:03,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38741/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38741/checkm_input OceanDNA-b38741/checkm_result
[2023-03-15 20:35:35,076] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:35,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.81%
Contamintation: 5.09%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-15 20:35:35,079] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:35,079] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:35,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38741/markers.fasta)
[2023-03-15 20:35:35,079] [INFO] Task started: Blastn
[2023-03-15 20:35:35,079] [INFO] Running command: blastn -query OceanDNA-b38741/markers.fasta -db /var/lib/cwl/stgd6782a55-a328-4dca-9282-dd5b99b6e8af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38741/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:35,862] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:35,863] [INFO] Selected 17 target genomes.
[2023-03-15 20:35:35,863] [INFO] Target genome list was writen to OceanDNA-b38741/target_genomes_gtdb.txt
[2023-03-15 20:35:36,223] [INFO] Task started: fastANI
[2023-03-15 20:35:36,223] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c60eba-613a-4eac-ba50-74f0419daf48/OceanDNA-b38741.fa --refList OceanDNA-b38741/target_genomes_gtdb.txt --output OceanDNA-b38741/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:45,251] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:45,256] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:45,257] [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_905182035.1	s__ASP10-02a sp905182035	82.0225	418	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002312935.1	s__ASP10-02a sp002312935	79.81	370	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.42	99.42	0.91	0.91	2	-
GCA_002470565.1	s__ASP10-02a sp002470565	78.8814	272	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.72	99.72	0.90	0.90	2	-
GCA_018647765.1	s__ASP10-02a sp018647765	78.4726	223	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.86	99.85	0.95	0.93	3	-
GCA_003523085.1	s__ASP10-02a sp003523085	78.1884	225	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335115.1	s__ASP10-02a sp002335115	78.0719	230	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.15	95.37	0.85	0.79	13	-
GCA_003521845.1	s__ASP10-02a sp003521845	76.255	63	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:45,257] [INFO] GTDB search result was written to OceanDNA-b38741/result_gtdb.tsv
[2023-03-15 20:35:45,257] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:45,258] [INFO] DFAST_QC result json was written to OceanDNA-b38741/dqc_result.json
[2023-03-15 20:35:45,258] [INFO] DFAST_QC completed!
[2023-03-15 20:35:45,258] [INFO] Total running time: 0h1m19s