[2023-06-04 19:38:30,607] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:38:30,612] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:38:30,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference
[2023-06-04 19:38:33,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:38:33,126] [INFO] Task started: Prodigal
[2023-06-04 19:38:33,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbfe1f8b-6920-47d6-8fa9-d742e1b3d654/GCA_934230095.1_ERR7738665_bin.336_genomic.fna.gz | prodigal -d GCA_934230095.1_ERR7738665_bin.336_genomic.fna/cds.fna -a GCA_934230095.1_ERR7738665_bin.336_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:35,666] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:35,667] [INFO] Task started: HMMsearch
[2023-06-04 19:38:35,667] [INFO] Running command: hmmsearch --tblout GCA_934230095.1_ERR7738665_bin.336_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference/reference_markers.hmm GCA_934230095.1_ERR7738665_bin.336_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:35,878] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:35,880] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdbfe1f8b-6920-47d6-8fa9-d742e1b3d654/GCA_934230095.1_ERR7738665_bin.336_genomic.fna.gz]
[2023-06-04 19:38:35,903] [INFO] Query marker FASTA was written to GCA_934230095.1_ERR7738665_bin.336_genomic.fna/markers.fasta
[2023-06-04 19:38:35,903] [INFO] Task started: Blastn
[2023-06-04 19:38:35,903] [INFO] Running command: blastn -query GCA_934230095.1_ERR7738665_bin.336_genomic.fna/markers.fasta -db /var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference/reference_markers.fasta -out GCA_934230095.1_ERR7738665_bin.336_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:38,154] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:38,158] [INFO] Selected 25 target genomes.
[2023-06-04 19:38:38,159] [INFO] Target genome list was writen to GCA_934230095.1_ERR7738665_bin.336_genomic.fna/target_genomes.txt
[2023-06-04 19:38:38,206] [INFO] Task started: fastANI
[2023-06-04 19:38:38,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbfe1f8b-6920-47d6-8fa9-d742e1b3d654/GCA_934230095.1_ERR7738665_bin.336_genomic.fna.gz --refList GCA_934230095.1_ERR7738665_bin.336_genomic.fna/target_genomes.txt --output GCA_934230095.1_ERR7738665_bin.336_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:48,802] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:48,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:48,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:48,806] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:48,806] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:38:48,807] [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
--------------------------------------------------------------------------------
[2023-06-04 19:38:48,811] [INFO] DFAST Taxonomy check result was written to GCA_934230095.1_ERR7738665_bin.336_genomic.fna/tc_result.tsv
[2023-06-04 19:38:48,812] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:48,812] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:48,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference/checkm_data
[2023-06-04 19:38:48,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:48,837] [INFO] Task started: CheckM
[2023-06-04 19:38:48,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934230095.1_ERR7738665_bin.336_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934230095.1_ERR7738665_bin.336_genomic.fna/checkm_input GCA_934230095.1_ERR7738665_bin.336_genomic.fna/checkm_result
[2023-06-04 19:39:04,855] [INFO] Task succeeded: CheckM
[2023-06-04 19:39:04,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:39:04,879] [INFO] ===== Completeness check finished =====
[2023-06-04 19:39:04,880] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:39:04,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934230095.1_ERR7738665_bin.336_genomic.fna/markers.fasta)
[2023-06-04 19:39:04,880] [INFO] Task started: Blastn
[2023-06-04 19:39:04,881] [INFO] Running command: blastn -query GCA_934230095.1_ERR7738665_bin.336_genomic.fna/markers.fasta -db /var/lib/cwl/stg9788beed-9620-490d-abfc-f543827ce228/dqc_reference/reference_markers_gtdb.fasta -out GCA_934230095.1_ERR7738665_bin.336_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:39:05,665] [INFO] Task succeeded: Blastn
[2023-06-04 19:39:05,670] [INFO] Selected 15 target genomes.
[2023-06-04 19:39:05,670] [INFO] Target genome list was writen to GCA_934230095.1_ERR7738665_bin.336_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:39:05,759] [INFO] Task started: fastANI
[2023-06-04 19:39:05,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbfe1f8b-6920-47d6-8fa9-d742e1b3d654/GCA_934230095.1_ERR7738665_bin.336_genomic.fna.gz --refList GCA_934230095.1_ERR7738665_bin.336_genomic.fna/target_genomes_gtdb.txt --output GCA_934230095.1_ERR7738665_bin.336_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:39:10,487] [INFO] Task succeeded: fastANI
[2023-06-04 19:39:10,493] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:39:10,493] [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_900754115.1	s__Caccosoma sp900754115	99.9256	435	463	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-631;g__Caccosoma	95.0	99.91	99.91	0.95	0.95	2	conclusive
GCA_000433015.1	s__Caccosoma faecigallinarum	82.1103	342	463	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-631;g__Caccosoma	95.0	98.21	98.10	0.86	0.80	5	-
GCA_905197115.1	s__Caccosoma sp905197115	78.1724	199	463	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-631;g__Caccosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:39:10,495] [INFO] GTDB search result was written to GCA_934230095.1_ERR7738665_bin.336_genomic.fna/result_gtdb.tsv
[2023-06-04 19:39:10,496] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:39:10,499] [INFO] DFAST_QC result json was written to GCA_934230095.1_ERR7738665_bin.336_genomic.fna/dqc_result.json
[2023-06-04 19:39:10,499] [INFO] DFAST_QC completed!
[2023-06-04 19:39:10,500] [INFO] Total running time: 0h0m40s