[2023-03-15 21:48:06,728] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference
[2023-03-15 21:48:07,847] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,847] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,848] [INFO] Running command: cat /var/lib/cwl/stg30565168-bf6e-4ad5-941c-43e733b4bab8/OceanDNA-b34262.fa | prodigal -d OceanDNA-b34262/cds.fna -a OceanDNA-b34262/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:31,209] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:31,210] [INFO] Task started: HMMsearch
[2023-03-15 21:48:31,210] [INFO] Running command: hmmsearch --tblout OceanDNA-b34262/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference/reference_markers.hmm OceanDNA-b34262/protein.faa > /dev/null
[2023-03-15 21:48:31,430] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:31,431] [INFO] Found 6/6 markers.
[2023-03-15 21:48:31,455] [INFO] Query marker FASTA was written to OceanDNA-b34262/markers.fasta
[2023-03-15 21:48:31,456] [INFO] Task started: Blastn
[2023-03-15 21:48:31,456] [INFO] Running command: blastn -query OceanDNA-b34262/markers.fasta -db /var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference/reference_markers.fasta -out OceanDNA-b34262/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:32,393] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:32,393] [INFO] Selected 25 target genomes.
[2023-03-15 21:48:32,394] [INFO] Target genome list was writen to OceanDNA-b34262/target_genomes.txt
[2023-03-15 21:48:32,525] [INFO] Task started: fastANI
[2023-03-15 21:48:32,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg30565168-bf6e-4ad5-941c-43e733b4bab8/OceanDNA-b34262.fa --refList OceanDNA-b34262/target_genomes.txt --output OceanDNA-b34262/fastani_result.tsv --threads 1
[2023-03-15 21:48:49,684] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:49,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:49,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:49,688] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:49,689] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:49,689] [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
Permianibacter aggregans	strain=DSM 103792	GCA_004363125.1	1510150	1510150	type	True	90.7697	1072	1218	95	below_threshold
Permianibacter aggregans	strain=HW001	GCA_009756665.1	1510150	1510150	type	True	90.735	1084	1218	95	below_threshold
Permianibacter fluminis	strain=IMCC34836	GCA_013179735.1	2738515	2738515	type	True	77.5957	263	1218	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:49,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34262/tc_result.tsv
[2023-03-15 21:48:49,690] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:49,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:49,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference/checkm_data
[2023-03-15 21:48:49,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:49,749] [INFO] Task started: CheckM
[2023-03-15 21:48:49,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34262/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34262/checkm_input OceanDNA-b34262/checkm_result
[2023-03-15 21:49:48,561] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:48,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:48,606] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:48,606] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:48,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34262/markers.fasta)
[2023-03-15 21:49:48,607] [INFO] Task started: Blastn
[2023-03-15 21:49:48,607] [INFO] Running command: blastn -query OceanDNA-b34262/markers.fasta -db /var/lib/cwl/stg73e0aabd-1d9a-4801-8091-c23726101177/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34262/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:49,879] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:49,886] [INFO] Selected 28 target genomes.
[2023-03-15 21:49:49,886] [INFO] Target genome list was writen to OceanDNA-b34262/target_genomes_gtdb.txt
[2023-03-15 21:49:49,994] [INFO] Task started: fastANI
[2023-03-15 21:49:49,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg30565168-bf6e-4ad5-941c-43e733b4bab8/OceanDNA-b34262.fa --refList OceanDNA-b34262/target_genomes_gtdb.txt --output OceanDNA-b34262/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:07,855] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:07,858] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:50:07,858] [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
GCF_009756665.1	s__Permianibacter aggregans	90.735	1084	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013179735.1	s__Permianibacter fluminis	77.5957	263	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	75.2954	55	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:07,859] [INFO] GTDB search result was written to OceanDNA-b34262/result_gtdb.tsv
[2023-03-15 21:50:07,860] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:07,862] [INFO] DFAST_QC result json was written to OceanDNA-b34262/dqc_result.json
[2023-03-15 21:50:07,862] [INFO] DFAST_QC completed!
[2023-03-15 21:50:07,862] [INFO] Total running time: 0h2m1s