[2023-03-15 21:24:38,451] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:38,451] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:38,451] [INFO] DQC Reference Directory: /var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference
[2023-03-15 21:24:39,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:39,528] [INFO] Task started: Prodigal
[2023-03-15 21:24:39,528] [INFO] Running command: cat /var/lib/cwl/stgee27452c-2540-4312-84c4-b7482408ddb4/OceanDNA-b38657.fa | prodigal -d OceanDNA-b38657/cds.fna -a OceanDNA-b38657/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:45,246] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:45,246] [INFO] Task started: HMMsearch
[2023-03-15 21:24:45,246] [INFO] Running command: hmmsearch --tblout OceanDNA-b38657/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference/reference_markers.hmm OceanDNA-b38657/protein.faa > /dev/null
[2023-03-15 21:24:45,396] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:45,396] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgee27452c-2540-4312-84c4-b7482408ddb4/OceanDNA-b38657.fa]
[2023-03-15 21:24:45,408] [INFO] Query marker FASTA was written to OceanDNA-b38657/markers.fasta
[2023-03-15 21:24:45,408] [INFO] Task started: Blastn
[2023-03-15 21:24:45,408] [INFO] Running command: blastn -query OceanDNA-b38657/markers.fasta -db /var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference/reference_markers.fasta -out OceanDNA-b38657/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:45,939] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:45,940] [INFO] Selected 21 target genomes.
[2023-03-15 21:24:45,940] [INFO] Target genome list was writen to OceanDNA-b38657/target_genomes.txt
[2023-03-15 21:24:45,951] [INFO] Task started: fastANI
[2023-03-15 21:24:45,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgee27452c-2540-4312-84c4-b7482408ddb4/OceanDNA-b38657.fa --refList OceanDNA-b38657/target_genomes.txt --output OceanDNA-b38657/fastani_result.tsv --threads 1
[2023-03-15 21:24:58,056] [INFO] Task succeeded: fastANI
[2023-03-15 21:24:58,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:24:58,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:24:58,057] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:24:58,057] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:24:58,057] [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 21:24:58,057] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38657/tc_result.tsv
[2023-03-15 21:24:58,058] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:24:58,058] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:24:58,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference/checkm_data
[2023-03-15 21:24:58,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:24:58,066] [INFO] Task started: CheckM
[2023-03-15 21:24:58,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38657/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38657/checkm_input OceanDNA-b38657/checkm_result
[2023-03-15 21:25:18,050] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:18,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:18,052] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:18,053] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:18,053] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38657/markers.fasta)
[2023-03-15 21:25:18,053] [INFO] Task started: Blastn
[2023-03-15 21:25:18,053] [INFO] Running command: blastn -query OceanDNA-b38657/markers.fasta -db /var/lib/cwl/stgc63fdbdb-c0c1-4981-bd96-cc6dccba9cca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38657/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:18,821] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:18,822] [INFO] Selected 15 target genomes.
[2023-03-15 21:25:18,822] [INFO] Target genome list was writen to OceanDNA-b38657/target_genomes_gtdb.txt
[2023-03-15 21:25:18,908] [INFO] Task started: fastANI
[2023-03-15 21:25:18,908] [INFO] Running command: fastANI --query /var/lib/cwl/stgee27452c-2540-4312-84c4-b7482408ddb4/OceanDNA-b38657.fa --refList OceanDNA-b38657/target_genomes_gtdb.txt --output OceanDNA-b38657/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:26,799] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:26,805] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:25:26,805] [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	78.1105	153	322	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	77.8067	142	322	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_002335115.1	s__ASP10-02a sp002335115	76.9849	123	322	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_002470565.1	s__ASP10-02a sp002470565	76.7959	86	322	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_003523085.1	s__ASP10-02a sp003523085	76.604	60	322	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 21:25:26,805] [INFO] GTDB search result was written to OceanDNA-b38657/result_gtdb.tsv
[2023-03-15 21:25:26,805] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:26,806] [INFO] DFAST_QC result json was written to OceanDNA-b38657/dqc_result.json
[2023-03-15 21:25:26,807] [INFO] DFAST_QC completed!
[2023-03-15 21:25:26,807] [INFO] Total running time: 0h0m48s