[2023-06-30 03:56:18,741] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:56:18,745] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:56:18,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference
[2023-06-30 03:56:20,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:56:20,003] [INFO] Task started: Prodigal
[2023-06-30 03:56:20,003] [INFO] Running command: gunzip -c /var/lib/cwl/stgaebb35d5-c537-4dea-a274-c8ec72afb126/GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna.gz | prodigal -d GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/cds.fna -a GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:56:32,941] [INFO] Task succeeded: Prodigal
[2023-06-30 03:56:32,941] [INFO] Task started: HMMsearch
[2023-06-30 03:56:32,941] [INFO] Running command: hmmsearch --tblout GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference/reference_markers.hmm GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:56:33,169] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:56:33,171] [INFO] Found 6/6 markers.
[2023-06-30 03:56:33,196] [INFO] Query marker FASTA was written to GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/markers.fasta
[2023-06-30 03:56:33,197] [INFO] Task started: Blastn
[2023-06-30 03:56:33,197] [INFO] Running command: blastn -query GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/markers.fasta -db /var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference/reference_markers.fasta -out GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:56:33,777] [INFO] Task succeeded: Blastn
[2023-06-30 03:56:33,780] [INFO] Selected 14 target genomes.
[2023-06-30 03:56:33,781] [INFO] Target genome list was writen to GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/target_genomes.txt
[2023-06-30 03:56:33,782] [INFO] Task started: fastANI
[2023-06-30 03:56:33,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgaebb35d5-c537-4dea-a274-c8ec72afb126/GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna.gz --refList GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/target_genomes.txt --output GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:56:43,351] [INFO] Task succeeded: fastANI
[2023-06-30 03:56:43,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:56:43,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:56:43,355] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:56:43,355] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 03:56:43,355] [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 03:56:43,357] [INFO] DFAST Taxonomy check result was written to GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/tc_result.tsv
[2023-06-30 03:56:43,358] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:56:43,358] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:56:43,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference/checkm_data
[2023-06-30 03:56:43,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:56:43,390] [INFO] Task started: CheckM
[2023-06-30 03:56:43,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/checkm_input GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/checkm_result
[2023-06-30 03:57:23,301] [INFO] Task succeeded: CheckM
[2023-06-30 03:57:23,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:57:23,322] [INFO] ===== Completeness check finished =====
[2023-06-30 03:57:23,323] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:57:23,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/markers.fasta)
[2023-06-30 03:57:23,323] [INFO] Task started: Blastn
[2023-06-30 03:57:23,323] [INFO] Running command: blastn -query GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/markers.fasta -db /var/lib/cwl/stg4afd3918-70bd-4554-9d27-a374fdf4d1ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:57:24,131] [INFO] Task succeeded: Blastn
[2023-06-30 03:57:24,137] [INFO] Selected 11 target genomes.
[2023-06-30 03:57:24,137] [INFO] Target genome list was writen to GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:57:24,161] [INFO] Task started: fastANI
[2023-06-30 03:57:24,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgaebb35d5-c537-4dea-a274-c8ec72afb126/GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna.gz --refList GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/target_genomes_gtdb.txt --output GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:57:30,565] [INFO] Task succeeded: fastANI
[2023-06-30 03:57:30,577] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:57:30,578] [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_903856085.1	s__XYB12-FULL-50-7 sp903856085	100.0	758	759	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__XYB12-FULL-50-7	95.0	99.96	99.95	0.97	0.96	3	conclusive
GCA_001804345.1	s__XYB12-FULL-50-7 sp001804345	81.2974	278	759	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__XYB12-FULL-50-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140935.1	s__XYB12-FULL-50-7 sp003140935	80.6053	359	759	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__XYB12-FULL-50-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884815.1	s__XYB12-FULL-50-7 sp903884815	78.8308	249	759	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__XYB12-FULL-50-7	95.0	99.89	99.82	0.98	0.97	7	-
GCA_903820505.1	s__CAIJHQ01 sp903820505	77.8187	140	759	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__CAIJHQ01	95.0	99.93	99.93	0.98	0.98	2	-
GCA_903819565.1	s__CAIJHQ01 sp903819565	76.7544	119	759	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__CAIJHQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:57:30,580] [INFO] GTDB search result was written to GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/result_gtdb.tsv
[2023-06-30 03:57:30,581] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:57:30,584] [INFO] DFAST_QC result json was written to GCA_903856085.1_freshwater_MAG_---_AM-2014-D6_bin-627_genomic.fna/dqc_result.json
[2023-06-30 03:57:30,584] [INFO] DFAST_QC completed!
[2023-06-30 03:57:30,584] [INFO] Total running time: 0h1m12s