[2023-03-17 11:38:03,654] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:38:03,654] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:38:03,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference
[2023-03-17 11:38:04,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:38:04,749] [INFO] Task started: Prodigal
[2023-03-17 11:38:04,750] [INFO] Running command: cat /var/lib/cwl/stgd8cbd3c4-b706-4046-b5e4-70a2a6184fb3/OceanDNA-b26523.fa | prodigal -d OceanDNA-b26523/cds.fna -a OceanDNA-b26523/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:38:15,191] [INFO] Task succeeded: Prodigal
[2023-03-17 11:38:15,191] [INFO] Task started: HMMsearch
[2023-03-17 11:38:15,191] [INFO] Running command: hmmsearch --tblout OceanDNA-b26523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference/reference_markers.hmm OceanDNA-b26523/protein.faa > /dev/null
[2023-03-17 11:38:15,375] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:38:15,376] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8cbd3c4-b706-4046-b5e4-70a2a6184fb3/OceanDNA-b26523.fa]
[2023-03-17 11:38:15,392] [INFO] Query marker FASTA was written to OceanDNA-b26523/markers.fasta
[2023-03-17 11:38:15,394] [INFO] Task started: Blastn
[2023-03-17 11:38:15,394] [INFO] Running command: blastn -query OceanDNA-b26523/markers.fasta -db /var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference/reference_markers.fasta -out OceanDNA-b26523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:15,994] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:15,995] [INFO] Selected 29 target genomes.
[2023-03-17 11:38:15,995] [INFO] Target genome list was writen to OceanDNA-b26523/target_genomes.txt
[2023-03-17 11:38:16,010] [INFO] Task started: fastANI
[2023-03-17 11:38:16,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8cbd3c4-b706-4046-b5e4-70a2a6184fb3/OceanDNA-b26523.fa --refList OceanDNA-b26523/target_genomes.txt --output OceanDNA-b26523/fastani_result.tsv --threads 1
[2023-03-17 11:38:35,341] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:35,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:38:35,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:38:35,341] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:38:35,341] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:38:35,341] [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 11:38:35,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26523/tc_result.tsv
[2023-03-17 11:38:35,346] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:38:35,346] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:38:35,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference/checkm_data
[2023-03-17 11:38:35,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:38:35,416] [INFO] Task started: CheckM
[2023-03-17 11:38:35,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26523/checkm_input OceanDNA-b26523/checkm_result
[2023-03-17 11:39:06,717] [INFO] Task succeeded: CheckM
[2023-03-17 11:39:06,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 11:39:06,733] [INFO] ===== Completeness check finished =====
[2023-03-17 11:39:06,733] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:39:06,734] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26523/markers.fasta)
[2023-03-17 11:39:06,734] [INFO] Task started: Blastn
[2023-03-17 11:39:06,735] [INFO] Running command: blastn -query OceanDNA-b26523/markers.fasta -db /var/lib/cwl/stg76e44d4b-2c9c-471f-b5b9-bc998e7e3a46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:39:07,664] [INFO] Task succeeded: Blastn
[2023-03-17 11:39:07,665] [INFO] Selected 13 target genomes.
[2023-03-17 11:39:07,665] [INFO] Target genome list was writen to OceanDNA-b26523/target_genomes_gtdb.txt
[2023-03-17 11:39:07,677] [INFO] Task started: fastANI
[2023-03-17 11:39:07,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8cbd3c4-b706-4046-b5e4-70a2a6184fb3/OceanDNA-b26523.fa --refList OceanDNA-b26523/target_genomes_gtdb.txt --output OceanDNA-b26523/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:39:12,598] [INFO] Task succeeded: fastANI
[2023-03-17 11:39:12,605] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:39:12,605] [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_002683535.1	s__UBA8309 sp002683535	97.341	284	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016780765.1	s__UBA8309 sp016780765	88.5673	395	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002686685.1	s__UBA8309 sp002686685	79.1955	225	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_009920665.1	s__UBA8309 sp009920665	78.5756	194	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	78.2867	196	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	78.0307	178	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	77.7798	145	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731315.1	s__UBA8309 sp002731315	77.7023	119	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.8452	82	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:39:12,605] [INFO] GTDB search result was written to OceanDNA-b26523/result_gtdb.tsv
[2023-03-17 11:39:12,605] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:39:12,606] [INFO] DFAST_QC result json was written to OceanDNA-b26523/dqc_result.json
[2023-03-17 11:39:12,606] [INFO] DFAST_QC completed!
[2023-03-17 11:39:12,606] [INFO] Total running time: 0h1m9s