[2023-06-30 05:03:15,958] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:03:15,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:03:15,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference
[2023-06-30 05:03:17,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:03:17,222] [INFO] Task started: Prodigal
[2023-06-30 05:03:17,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg9393ca64-bc97-4d83-81f5-71c198fbc3c5/GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna.gz | prodigal -d GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/cds.fna -a GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:03:20,891] [INFO] Task succeeded: Prodigal
[2023-06-30 05:03:20,892] [INFO] Task started: HMMsearch
[2023-06-30 05:03:20,892] [INFO] Running command: hmmsearch --tblout GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference/reference_markers.hmm GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:03:21,117] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:03:21,119] [INFO] Found 6/6 markers.
[2023-06-30 05:03:21,150] [INFO] Query marker FASTA was written to GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/markers.fasta
[2023-06-30 05:03:21,150] [INFO] Task started: Blastn
[2023-06-30 05:03:21,150] [INFO] Running command: blastn -query GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/markers.fasta -db /var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference/reference_markers.fasta -out GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:03:21,734] [INFO] Task succeeded: Blastn
[2023-06-30 05:03:21,739] [INFO] Selected 15 target genomes.
[2023-06-30 05:03:21,739] [INFO] Target genome list was writen to GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/target_genomes.txt
[2023-06-30 05:03:21,741] [INFO] Task started: fastANI
[2023-06-30 05:03:21,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg9393ca64-bc97-4d83-81f5-71c198fbc3c5/GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna.gz --refList GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/target_genomes.txt --output GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:03:31,031] [INFO] Task succeeded: fastANI
[2023-06-30 05:03:31,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:03:31,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:03:31,034] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:03:31,034] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:03:31,034] [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
--------------------------------------------------------------------------------
[2023-06-30 05:03:31,037] [INFO] DFAST Taxonomy check result was written to GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/tc_result.tsv
[2023-06-30 05:03:31,038] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:03:31,038] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:03:31,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference/checkm_data
[2023-06-30 05:03:31,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:03:31,066] [INFO] Task started: CheckM
[2023-06-30 05:03:31,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/checkm_input GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/checkm_result
[2023-06-30 05:03:49,876] [INFO] Task succeeded: CheckM
[2023-06-30 05:03:49,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:03:49,897] [INFO] ===== Completeness check finished =====
[2023-06-30 05:03:49,897] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:03:49,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/markers.fasta)
[2023-06-30 05:03:49,898] [INFO] Task started: Blastn
[2023-06-30 05:03:49,898] [INFO] Running command: blastn -query GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/markers.fasta -db /var/lib/cwl/stgea89e9b4-11a8-4078-81b0-a0ced8e940a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:03:50,875] [INFO] Task succeeded: Blastn
[2023-06-30 05:03:50,879] [INFO] Selected 6 target genomes.
[2023-06-30 05:03:50,879] [INFO] Target genome list was writen to GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:03:50,880] [INFO] Task started: fastANI
[2023-06-30 05:03:50,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg9393ca64-bc97-4d83-81f5-71c198fbc3c5/GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna.gz --refList GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/target_genomes_gtdb.txt --output GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:03:54,348] [INFO] Task succeeded: fastANI
[2023-06-30 05:03:54,355] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:03:54,355] [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_903861835.1	s__CAIOVX01 sp903861835	99.9527	498	513	d__Bacteria;p__Firestonebacteria;c__D2-FULL-39-29;o__D2-FULL-39-29;f__CAIOVX01;g__CAIOVX01	95.0	99.79	99.67	0.96	0.94	16	conclusive
GCA_903915125.1	s__CAIOVX01 sp903915125	83.0275	330	513	d__Bacteria;p__Firestonebacteria;c__D2-FULL-39-29;o__D2-FULL-39-29;f__CAIOVX01;g__CAIOVX01	95.0	99.69	99.52	0.87	0.83	7	-
GCA_903916325.1	s__CAIOVX01 sp903916325	82.1753	329	513	d__Bacteria;p__Firestonebacteria;c__D2-FULL-39-29;o__D2-FULL-39-29;f__CAIOVX01;g__CAIOVX01	95.0	99.59	99.52	0.83	0.81	5	-
GCA_903894145.1	s__CAIOVX01 sp903894145	82.0646	301	513	d__Bacteria;p__Firestonebacteria;c__D2-FULL-39-29;o__D2-FULL-39-29;f__CAIOVX01;g__CAIOVX01	95.0	99.91	99.83	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2023-06-30 05:03:54,357] [INFO] GTDB search result was written to GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/result_gtdb.tsv
[2023-06-30 05:03:54,358] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:03:54,361] [INFO] DFAST_QC result json was written to GCA_903855845.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0028_genomic.fna/dqc_result.json
[2023-06-30 05:03:54,361] [INFO] DFAST_QC completed!
[2023-06-30 05:03:54,361] [INFO] Total running time: 0h0m38s