[2023-06-30 20:55:36,067] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:55:36,069] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:55:36,069] [INFO] DQC Reference Directory: /var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference
[2023-06-30 20:55:37,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:55:37,362] [INFO] Task started: Prodigal
[2023-06-30 20:55:37,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg01c6a900-2272-43f1-9437-a92cbdf193f9/GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna.gz | prodigal -d GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/cds.fna -a GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:55:43,179] [INFO] Task succeeded: Prodigal
[2023-06-30 20:55:43,179] [INFO] Task started: HMMsearch
[2023-06-30 20:55:43,179] [INFO] Running command: hmmsearch --tblout GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference/reference_markers.hmm GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:55:43,390] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:55:43,391] [INFO] Found 6/6 markers.
[2023-06-30 20:55:43,420] [INFO] Query marker FASTA was written to GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/markers.fasta
[2023-06-30 20:55:43,420] [INFO] Task started: Blastn
[2023-06-30 20:55:43,420] [INFO] Running command: blastn -query GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/markers.fasta -db /var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference/reference_markers.fasta -out GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:44,022] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:44,027] [INFO] Selected 16 target genomes.
[2023-06-30 20:55:44,028] [INFO] Target genome list was writen to GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/target_genomes.txt
[2023-06-30 20:55:44,030] [INFO] Task started: fastANI
[2023-06-30 20:55:44,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c6a900-2272-43f1-9437-a92cbdf193f9/GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna.gz --refList GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/target_genomes.txt --output GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:55:51,772] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:51,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:55:51,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:55:51,775] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:55:51,775] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:55:51,775] [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 20:55:51,777] [INFO] DFAST Taxonomy check result was written to GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/tc_result.tsv
[2023-06-30 20:55:51,777] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:55:51,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:55:51,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference/checkm_data
[2023-06-30 20:55:51,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:55:51,808] [INFO] Task started: CheckM
[2023-06-30 20:55:51,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/checkm_input GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/checkm_result
[2023-06-30 20:56:15,204] [INFO] Task succeeded: CheckM
[2023-06-30 20:56:15,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-30 20:56:15,223] [INFO] ===== Completeness check finished =====
[2023-06-30 20:56:15,224] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:56:15,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/markers.fasta)
[2023-06-30 20:56:15,224] [INFO] Task started: Blastn
[2023-06-30 20:56:15,224] [INFO] Running command: blastn -query GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/markers.fasta -db /var/lib/cwl/stgee178a2e-45c4-4f73-a9c4-f8cf8800f320/dqc_reference/reference_markers_gtdb.fasta -out GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:56:16,156] [INFO] Task succeeded: Blastn
[2023-06-30 20:56:16,159] [INFO] Selected 17 target genomes.
[2023-06-30 20:56:16,159] [INFO] Target genome list was writen to GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:56:16,164] [INFO] Task started: fastANI
[2023-06-30 20:56:16,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c6a900-2272-43f1-9437-a92cbdf193f9/GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna.gz --refList GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/target_genomes_gtdb.txt --output GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:56:23,869] [INFO] Task succeeded: fastANI
[2023-06-30 20:56:23,873] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:56:23,873] [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_903822335.1	s__CAIJOT01 sp903822335	100.0	768	779	d__Bacteria;p__Desulfobacterota_G;c__Syntrophorhabdia;o__Syntrophorhabdales;f__Syntrophorhabdaceae;g__CAIJOT01	95.0	99.58	99.56	0.87	0.87	3	conclusive
GCA_013824835.1	s__PNOM01 sp013824835	76.2623	54	779	d__Bacteria;p__Desulfobacterota_G;c__Syntrophorhabdia;o__Syntrophorhabdales;f__Syntrophorhabdaceae;g__PNOM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:56:23,875] [INFO] GTDB search result was written to GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/result_gtdb.tsv
[2023-06-30 20:56:23,876] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:56:23,878] [INFO] DFAST_QC result json was written to GCA_903822335.1_freshwater_MAG_---_AlinenSediments_bin-2384_genomic.fna/dqc_result.json
[2023-06-30 20:56:23,878] [INFO] DFAST_QC completed!
[2023-06-30 20:56:23,878] [INFO] Total running time: 0h0m48s