[2023-03-16 15:26:08,184] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,184] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference
[2023-03-16 15:26:09,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:09,503] [INFO] Task started: Prodigal
[2023-03-16 15:26:09,504] [INFO] Running command: cat /var/lib/cwl/stg3c19fd82-33f7-4fee-a30e-6eadc64e13fe/OceanDNA-b42464.fa | prodigal -d OceanDNA-b42464/cds.fna -a OceanDNA-b42464/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:14,936] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:14,936] [INFO] Task started: HMMsearch
[2023-03-16 15:26:14,936] [INFO] Running command: hmmsearch --tblout OceanDNA-b42464/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference/reference_markers.hmm OceanDNA-b42464/protein.faa > /dev/null
[2023-03-16 15:26:15,091] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:15,091] [INFO] Found 6/6 markers.
[2023-03-16 15:26:15,101] [INFO] Query marker FASTA was written to OceanDNA-b42464/markers.fasta
[2023-03-16 15:26:15,101] [INFO] Task started: Blastn
[2023-03-16 15:26:15,101] [INFO] Running command: blastn -query OceanDNA-b42464/markers.fasta -db /var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference/reference_markers.fasta -out OceanDNA-b42464/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:15,655] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:15,656] [INFO] Selected 16 target genomes.
[2023-03-16 15:26:15,656] [INFO] Target genome list was writen to OceanDNA-b42464/target_genomes.txt
[2023-03-16 15:26:15,664] [INFO] Task started: fastANI
[2023-03-16 15:26:15,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c19fd82-33f7-4fee-a30e-6eadc64e13fe/OceanDNA-b42464.fa --refList OceanDNA-b42464/target_genomes.txt --output OceanDNA-b42464/fastani_result.tsv --threads 1
[2023-03-16 15:26:27,780] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:27,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:27,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:27,781] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:27,781] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 15:26:27,781] [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 15:26:27,781] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42464/tc_result.tsv
[2023-03-16 15:26:27,781] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:27,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:27,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference/checkm_data
[2023-03-16 15:26:27,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:27,788] [INFO] Task started: CheckM
[2023-03-16 15:26:27,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42464/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42464/checkm_input OceanDNA-b42464/checkm_result
[2023-03-16 15:26:54,977] [INFO] Task succeeded: CheckM
[2023-03-16 15:26:54,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:26:54,979] [INFO] ===== Completeness check finished =====
[2023-03-16 15:26:54,979] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:26:54,979] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42464/markers.fasta)
[2023-03-16 15:26:54,980] [INFO] Task started: Blastn
[2023-03-16 15:26:54,980] [INFO] Running command: blastn -query OceanDNA-b42464/markers.fasta -db /var/lib/cwl/stg15ae8e22-9bc0-46d7-aee5-4b625d6926f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42464/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:55,867] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:55,868] [INFO] Selected 22 target genomes.
[2023-03-16 15:26:55,868] [INFO] Target genome list was writen to OceanDNA-b42464/target_genomes_gtdb.txt
[2023-03-16 15:26:56,600] [INFO] Task started: fastANI
[2023-03-16 15:26:56,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c19fd82-33f7-4fee-a30e-6eadc64e13fe/OceanDNA-b42464.fa --refList OceanDNA-b42464/target_genomes_gtdb.txt --output OceanDNA-b42464/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:27:01,519] [INFO] Task succeeded: fastANI
[2023-03-16 15:27:01,525] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:27:01,525] [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_016777005.1	s__GCA-2707915 sp016777005	93.8081	251	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214065.1	s__GCA-2707915 sp004214065	78.0119	112	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
GCA_902517565.1	s__GCA-2707915 sp902517565	77.8697	95	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212335.1	s__GCA-2707915 sp003212335	77.7475	109	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.3312	90	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574355.1	s__GCA-2707915 sp902574355	77.2444	94	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514295.1	s__GCA-2730855 sp902514295	77.0405	52	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606175.1	s__GCA-2707915 sp902606175	76.9878	92	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	-
GCA_902620785.1	s__GCA-2707915 sp902620785	76.8697	104	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
--------------------------------------------------------------------------------
[2023-03-16 15:27:01,525] [INFO] GTDB search result was written to OceanDNA-b42464/result_gtdb.tsv
[2023-03-16 15:27:01,525] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:27:01,526] [INFO] DFAST_QC result json was written to OceanDNA-b42464/dqc_result.json
[2023-03-16 15:27:01,526] [INFO] DFAST_QC completed!
[2023-03-16 15:27:01,526] [INFO] Total running time: 0h0m53s