[2023-03-17 03:50:13,844] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,844] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference
[2023-03-17 03:50:15,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,102] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,102] [INFO] Running command: cat /var/lib/cwl/stgc1173c00-a5c7-45e0-8a42-388034a2dd35/OceanDNA-b38660.fa | prodigal -d OceanDNA-b38660/cds.fna -a OceanDNA-b38660/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:24,886] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:24,886] [INFO] Task started: HMMsearch
[2023-03-17 03:50:24,886] [INFO] Running command: hmmsearch --tblout OceanDNA-b38660/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference/reference_markers.hmm OceanDNA-b38660/protein.faa > /dev/null
[2023-03-17 03:50:25,072] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:25,073] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc1173c00-a5c7-45e0-8a42-388034a2dd35/OceanDNA-b38660.fa]
[2023-03-17 03:50:25,085] [INFO] Query marker FASTA was written to OceanDNA-b38660/markers.fasta
[2023-03-17 03:50:25,085] [INFO] Task started: Blastn
[2023-03-17 03:50:25,086] [INFO] Running command: blastn -query OceanDNA-b38660/markers.fasta -db /var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference/reference_markers.fasta -out OceanDNA-b38660/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:25,667] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:25,668] [INFO] Selected 31 target genomes.
[2023-03-17 03:50:25,668] [INFO] Target genome list was writen to OceanDNA-b38660/target_genomes.txt
[2023-03-17 03:50:25,687] [INFO] Task started: fastANI
[2023-03-17 03:50:25,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1173c00-a5c7-45e0-8a42-388034a2dd35/OceanDNA-b38660.fa --refList OceanDNA-b38660/target_genomes.txt --output OceanDNA-b38660/fastani_result.tsv --threads 1
[2023-03-17 03:50:45,241] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:45,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:45,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:45,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:45,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:50:45,242] [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
--------------------------------------------------------------------------------
[2023-03-17 03:50:45,242] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38660/tc_result.tsv
[2023-03-17 03:50:45,242] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:45,242] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:45,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference/checkm_data
[2023-03-17 03:50:45,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:45,248] [INFO] Task started: CheckM
[2023-03-17 03:50:45,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38660/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38660/checkm_input OceanDNA-b38660/checkm_result
[2023-03-17 03:51:13,679] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:13,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:13,681] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:13,681] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:13,682] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38660/markers.fasta)
[2023-03-17 03:51:13,682] [INFO] Task started: Blastn
[2023-03-17 03:51:13,682] [INFO] Running command: blastn -query OceanDNA-b38660/markers.fasta -db /var/lib/cwl/stg70fa0eff-f8e4-47d4-8ce3-4c01d871c8bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38660/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:14,631] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:14,632] [INFO] Selected 20 target genomes.
[2023-03-17 03:51:14,632] [INFO] Target genome list was writen to OceanDNA-b38660/target_genomes_gtdb.txt
[2023-03-17 03:51:14,852] [INFO] Task started: fastANI
[2023-03-17 03:51:14,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1173c00-a5c7-45e0-8a42-388034a2dd35/OceanDNA-b38660.fa --refList OceanDNA-b38660/target_genomes_gtdb.txt --output OceanDNA-b38660/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:25,026] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:25,030] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:51:25,030] [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_002686055.1	s__ASP10-02a sp002686055	91.3851	370	582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.76	99.76	0.70	0.70	2	-
GCA_003497765.1	s__ASP10-02a sp003497765	90.3079	349	582	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	77.3851	126	582	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_016845445.1	s__ASP10-02a sp016845445	77.1226	92	582	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_003523085.1	s__ASP10-02a sp003523085	76.2268	50	582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:25,030] [INFO] GTDB search result was written to OceanDNA-b38660/result_gtdb.tsv
[2023-03-17 03:51:25,030] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:25,031] [INFO] DFAST_QC result json was written to OceanDNA-b38660/dqc_result.json
[2023-03-17 03:51:25,031] [INFO] DFAST_QC completed!
[2023-03-17 03:51:25,031] [INFO] Total running time: 0h1m11s