[2023-03-18 08:31:56,311] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,311] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference
[2023-03-18 08:31:57,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,411] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,411] [INFO] Running command: cat /var/lib/cwl/stg222651a5-888b-4188-9e0c-87934df49f0c/OceanDNA-b38718.fa | prodigal -d OceanDNA-b38718/cds.fna -a OceanDNA-b38718/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:10,664] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:10,665] [INFO] Task started: HMMsearch
[2023-03-18 08:32:10,665] [INFO] Running command: hmmsearch --tblout OceanDNA-b38718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference/reference_markers.hmm OceanDNA-b38718/protein.faa > /dev/null
[2023-03-18 08:32:10,850] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:10,850] [INFO] Found 6/6 markers.
[2023-03-18 08:32:10,866] [INFO] Query marker FASTA was written to OceanDNA-b38718/markers.fasta
[2023-03-18 08:32:10,867] [INFO] Task started: Blastn
[2023-03-18 08:32:10,867] [INFO] Running command: blastn -query OceanDNA-b38718/markers.fasta -db /var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference/reference_markers.fasta -out OceanDNA-b38718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:11,399] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:11,399] [INFO] Selected 29 target genomes.
[2023-03-18 08:32:11,400] [INFO] Target genome list was writen to OceanDNA-b38718/target_genomes.txt
[2023-03-18 08:32:11,413] [INFO] Task started: fastANI
[2023-03-18 08:32:11,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg222651a5-888b-4188-9e0c-87934df49f0c/OceanDNA-b38718.fa --refList OceanDNA-b38718/target_genomes.txt --output OceanDNA-b38718/fastani_result.tsv --threads 1
[2023-03-18 08:32:26,523] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:26,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:26,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:26,524] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:26,524] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:32:26,524] [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
--------------------------------------------------------------------------------
[2023-03-18 08:32:26,524] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38718/tc_result.tsv
[2023-03-18 08:32:26,524] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:26,524] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:26,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference/checkm_data
[2023-03-18 08:32:26,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:26,572] [INFO] Task started: CheckM
[2023-03-18 08:32:26,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38718/checkm_input OceanDNA-b38718/checkm_result
[2023-03-18 08:33:02,441] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:02,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:02,444] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:02,444] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:02,444] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38718/markers.fasta)
[2023-03-18 08:33:02,444] [INFO] Task started: Blastn
[2023-03-18 08:33:02,444] [INFO] Running command: blastn -query OceanDNA-b38718/markers.fasta -db /var/lib/cwl/stgf0478e2c-b79b-44ef-8db3-61611bfc8ae4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:03,167] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:03,168] [INFO] Selected 15 target genomes.
[2023-03-18 08:33:03,168] [INFO] Target genome list was writen to OceanDNA-b38718/target_genomes_gtdb.txt
[2023-03-18 08:33:03,270] [INFO] Task started: fastANI
[2023-03-18 08:33:03,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg222651a5-888b-4188-9e0c-87934df49f0c/OceanDNA-b38718.fa --refList OceanDNA-b38718/target_genomes_gtdb.txt --output OceanDNA-b38718/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:10,996] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:11,001] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:33:11,001] [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_002312935.1	s__ASP10-02a sp002312935	94.6261	623	793	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_905182035.1	s__ASP10-02a sp905182035	81.3042	495	793	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_002470565.1	s__ASP10-02a sp002470565	79.4267	334	793	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	78.6622	216	793	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_002335115.1	s__ASP10-02a sp002335115	78.5264	290	793	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_003523085.1	s__ASP10-02a sp003523085	78.4569	206	793	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_003521845.1	s__ASP10-02a sp003521845	76.1725	73	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:11,001] [INFO] GTDB search result was written to OceanDNA-b38718/result_gtdb.tsv
[2023-03-18 08:33:11,001] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:11,002] [INFO] DFAST_QC result json was written to OceanDNA-b38718/dqc_result.json
[2023-03-18 08:33:11,002] [INFO] DFAST_QC completed!
[2023-03-18 08:33:11,002] [INFO] Total running time: 0h1m15s