[2023-03-16 05:09:10,956] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,956] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,956] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference
[2023-03-16 05:09:12,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,034] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,035] [INFO] Running command: cat /var/lib/cwl/stgf90c59a6-3f2d-4c67-b364-e7941edc0bda/OceanDNA-b38742.fa | prodigal -d OceanDNA-b38742/cds.fna -a OceanDNA-b38742/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:23,594] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:23,594] [INFO] Task started: HMMsearch
[2023-03-16 05:09:23,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b38742/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference/reference_markers.hmm OceanDNA-b38742/protein.faa > /dev/null
[2023-03-16 05:09:23,750] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:23,750] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf90c59a6-3f2d-4c67-b364-e7941edc0bda/OceanDNA-b38742.fa]
[2023-03-16 05:09:23,765] [INFO] Query marker FASTA was written to OceanDNA-b38742/markers.fasta
[2023-03-16 05:09:23,767] [INFO] Task started: Blastn
[2023-03-16 05:09:23,767] [INFO] Running command: blastn -query OceanDNA-b38742/markers.fasta -db /var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference/reference_markers.fasta -out OceanDNA-b38742/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:24,265] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:24,266] [INFO] Selected 19 target genomes.
[2023-03-16 05:09:24,266] [INFO] Target genome list was writen to OceanDNA-b38742/target_genomes.txt
[2023-03-16 05:09:24,276] [INFO] Task started: fastANI
[2023-03-16 05:09:24,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgf90c59a6-3f2d-4c67-b364-e7941edc0bda/OceanDNA-b38742.fa --refList OceanDNA-b38742/target_genomes.txt --output OceanDNA-b38742/fastani_result.tsv --threads 1
[2023-03-16 05:09:34,918] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:34,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:34,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:34,919] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:34,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:09:34,919] [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
--------------------------------------------------------------------------------
[2023-03-16 05:09:34,919] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38742/tc_result.tsv
[2023-03-16 05:09:34,919] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:34,919] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:34,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference/checkm_data
[2023-03-16 05:09:34,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:34,926] [INFO] Task started: CheckM
[2023-03-16 05:09:34,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38742/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38742/checkm_input OceanDNA-b38742/checkm_result
[2023-03-16 05:10:07,334] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:07,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:07,337] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:07,337] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:07,337] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38742/markers.fasta)
[2023-03-16 05:10:07,338] [INFO] Task started: Blastn
[2023-03-16 05:10:07,338] [INFO] Running command: blastn -query OceanDNA-b38742/markers.fasta -db /var/lib/cwl/stgf3a414c3-155f-41a1-b8b3-69ad105d4403/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38742/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:07,981] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:07,982] [INFO] Selected 16 target genomes.
[2023-03-16 05:10:07,982] [INFO] Target genome list was writen to OceanDNA-b38742/target_genomes_gtdb.txt
[2023-03-16 05:10:08,057] [INFO] Task started: fastANI
[2023-03-16 05:10:08,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgf90c59a6-3f2d-4c67-b364-e7941edc0bda/OceanDNA-b38742.fa --refList OceanDNA-b38742/target_genomes_gtdb.txt --output OceanDNA-b38742/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:16,125] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:16,129] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:10:16,130] [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	81.7719	434	694	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	80.0927	360	694	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	78.9538	280	694	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	78.4179	223	694	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	78.3688	213	694	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	77.611	255	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.15	95.37	0.85	0.79	13	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:16,130] [INFO] GTDB search result was written to OceanDNA-b38742/result_gtdb.tsv
[2023-03-16 05:10:16,131] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:16,132] [INFO] DFAST_QC result json was written to OceanDNA-b38742/dqc_result.json
[2023-03-16 05:10:16,132] [INFO] DFAST_QC completed!
[2023-03-16 05:10:16,132] [INFO] Total running time: 0h1m5s