[2023-03-16 08:58:01,914] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:58:01,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:58:01,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference
[2023-03-16 08:58:03,037] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:58:03,038] [INFO] Task started: Prodigal
[2023-03-16 08:58:03,038] [INFO] Running command: cat /var/lib/cwl/stgaef55357-28be-4b1b-9d26-5c2f42c1aafe/OceanDNA-b40225.fa | prodigal -d OceanDNA-b40225/cds.fna -a OceanDNA-b40225/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:58:10,680] [INFO] Task succeeded: Prodigal
[2023-03-16 08:58:10,680] [INFO] Task started: HMMsearch
[2023-03-16 08:58:10,680] [INFO] Running command: hmmsearch --tblout OceanDNA-b40225/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference/reference_markers.hmm OceanDNA-b40225/protein.faa > /dev/null
[2023-03-16 08:58:10,865] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:58:10,866] [INFO] Found 6/6 markers.
[2023-03-16 08:58:10,886] [INFO] Query marker FASTA was written to OceanDNA-b40225/markers.fasta
[2023-03-16 08:58:10,888] [INFO] Task started: Blastn
[2023-03-16 08:58:10,888] [INFO] Running command: blastn -query OceanDNA-b40225/markers.fasta -db /var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference/reference_markers.fasta -out OceanDNA-b40225/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:58:11,552] [INFO] Task succeeded: Blastn
[2023-03-16 08:58:11,555] [INFO] Selected 25 target genomes.
[2023-03-16 08:58:11,555] [INFO] Target genome list was writen to OceanDNA-b40225/target_genomes.txt
[2023-03-16 08:58:11,577] [INFO] Task started: fastANI
[2023-03-16 08:58:11,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef55357-28be-4b1b-9d26-5c2f42c1aafe/OceanDNA-b40225.fa --refList OceanDNA-b40225/target_genomes.txt --output OceanDNA-b40225/fastani_result.tsv --threads 1
[2023-03-16 08:58:24,696] [INFO] Task succeeded: fastANI
[2023-03-16 08:58:24,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:58:24,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:58:24,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:58:24,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:58:24,697] [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 08:58:24,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40225/tc_result.tsv
[2023-03-16 08:58:24,697] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:58:24,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:58:24,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference/checkm_data
[2023-03-16 08:58:24,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:58:24,703] [INFO] Task started: CheckM
[2023-03-16 08:58:24,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40225/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40225/checkm_input OceanDNA-b40225/checkm_result
[2023-03-16 08:58:50,292] [INFO] Task succeeded: CheckM
[2023-03-16 08:58:50,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:58:50,294] [INFO] ===== Completeness check finished =====
[2023-03-16 08:58:50,294] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:58:50,294] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40225/markers.fasta)
[2023-03-16 08:58:50,295] [INFO] Task started: Blastn
[2023-03-16 08:58:50,295] [INFO] Running command: blastn -query OceanDNA-b40225/markers.fasta -db /var/lib/cwl/stg2c388c42-dc83-486d-b0b2-4e1914aab24a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40225/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:58:51,425] [INFO] Task succeeded: Blastn
[2023-03-16 08:58:51,426] [INFO] Selected 9 target genomes.
[2023-03-16 08:58:51,426] [INFO] Target genome list was writen to OceanDNA-b40225/target_genomes_gtdb.txt
[2023-03-16 08:58:51,439] [INFO] Task started: fastANI
[2023-03-16 08:58:51,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef55357-28be-4b1b-9d26-5c2f42c1aafe/OceanDNA-b40225.fa --refList OceanDNA-b40225/target_genomes_gtdb.txt --output OceanDNA-b40225/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:58:55,642] [INFO] Task succeeded: fastANI
[2023-03-16 08:58:55,647] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:58:55,647] [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_002720735.1	s__TMED48 sp002720735	98.952	412	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	97.48	96.80	0.75	0.75	3	conclusive
GCA_902562425.1	s__TMED48 sp902562425	94.5065	410	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	99.92	99.92	0.89	0.89	2	-
GCA_002338445.1	s__TMED48 sp002338445	92.8404	414	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689135.1	s__TMED48 sp002689135	81.9261	274	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	99.93	99.93	0.80	0.80	2	-
GCA_002731695.1	s__TMED48 sp002731695	81.6547	353	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691825.1	s__TMED48 sp002691825	81.2617	301	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:58:55,647] [INFO] GTDB search result was written to OceanDNA-b40225/result_gtdb.tsv
[2023-03-16 08:58:55,647] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:58:55,648] [INFO] DFAST_QC result json was written to OceanDNA-b40225/dqc_result.json
[2023-03-16 08:58:55,648] [INFO] DFAST_QC completed!
[2023-03-16 08:58:55,648] [INFO] Total running time: 0h0m54s