[2023-07-01 06:19:07,472] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:19:07,491] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:19:07,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference
[2023-07-01 06:19:08,803] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:19:08,804] [INFO] Task started: Prodigal
[2023-07-01 06:19:08,804] [INFO] Running command: gunzip -c /var/lib/cwl/stg18855d51-48b8-4f00-a024-18299c1d76f8/GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna.gz | prodigal -d GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/cds.fna -a GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:19:10,631] [INFO] Task succeeded: Prodigal
[2023-07-01 06:19:10,632] [INFO] Task started: HMMsearch
[2023-07-01 06:19:10,632] [INFO] Running command: hmmsearch --tblout GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference/reference_markers.hmm GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:19:10,815] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:19:10,816] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg18855d51-48b8-4f00-a024-18299c1d76f8/GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna.gz]
[2023-07-01 06:19:10,833] [INFO] Query marker FASTA was written to GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/markers.fasta
[2023-07-01 06:19:10,833] [INFO] Task started: Blastn
[2023-07-01 06:19:10,833] [INFO] Running command: blastn -query GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/markers.fasta -db /var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference/reference_markers.fasta -out GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:19:11,372] [INFO] Task succeeded: Blastn
[2023-07-01 06:19:11,377] [INFO] Selected 6 target genomes.
[2023-07-01 06:19:11,378] [INFO] Target genome list was writen to GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/target_genomes.txt
[2023-07-01 06:19:11,380] [INFO] Task started: fastANI
[2023-07-01 06:19:11,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg18855d51-48b8-4f00-a024-18299c1d76f8/GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna.gz --refList GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/target_genomes.txt --output GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:19:13,194] [INFO] Task succeeded: fastANI
[2023-07-01 06:19:13,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:19:13,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:19:13,196] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:19:13,196] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 06:19:13,197] [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
--------------------------------------------------------------------------------
[2023-07-01 06:19:13,199] [INFO] DFAST Taxonomy check result was written to GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/tc_result.tsv
[2023-07-01 06:19:13,199] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:19:13,200] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:19:13,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference/checkm_data
[2023-07-01 06:19:13,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:19:13,223] [INFO] Task started: CheckM
[2023-07-01 06:19:13,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/checkm_input GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/checkm_result
[2023-07-01 06:19:29,866] [INFO] Task succeeded: CheckM
[2023-07-01 06:19:29,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:19:29,886] [INFO] ===== Completeness check finished =====
[2023-07-01 06:19:29,886] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:19:29,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/markers.fasta)
[2023-07-01 06:19:29,887] [INFO] Task started: Blastn
[2023-07-01 06:19:29,887] [INFO] Running command: blastn -query GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/markers.fasta -db /var/lib/cwl/stg99f5dcdc-9ebe-4f48-ae0c-21720e4319a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:19:30,594] [INFO] Task succeeded: Blastn
[2023-07-01 06:19:30,626] [INFO] Selected 8 target genomes.
[2023-07-01 06:19:30,627] [INFO] Target genome list was writen to GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:19:30,663] [INFO] Task started: fastANI
[2023-07-01 06:19:30,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg18855d51-48b8-4f00-a024-18299c1d76f8/GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna.gz --refList GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/target_genomes_gtdb.txt --output GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:19:32,894] [INFO] Task succeeded: fastANI
[2023-07-01 06:19:32,904] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:19:32,904] [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_002346305.1	s__UBA3012 sp002346305	91.0898	104	118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	95.05	95.05	0.74	0.74	2	-
GCA_903902965.1	s__UBA3012 sp903902965	86.9868	97	118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	99.39	99.39	0.86	0.86	2	-
GCA_009701305.1	s__UBA3012 sp009701305	85.4707	95	118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	99.65	99.63	0.87	0.87	3	-
GCA_014190175.1	s__UBA3012 sp014190175	85.1435	102	118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694285.1	s__UBA3012 sp009694285	84.561	102	118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010031635.1	s__UBA3012 sp010031635	83.589	96	118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:19:32,906] [INFO] GTDB search result was written to GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/result_gtdb.tsv
[2023-07-01 06:19:32,907] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:19:32,909] [INFO] DFAST_QC result json was written to GCA_903855455.1_freshwater_MAG_---_Erken-D11_bin-0214_genomic.fna/dqc_result.json
[2023-07-01 06:19:32,910] [INFO] DFAST_QC completed!
[2023-07-01 06:19:32,910] [INFO] Total running time: 0h0m25s