[2023-06-05 06:18:33,243] [INFO] DFAST_QC pipeline started.
[2023-06-05 06:18:33,246] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 06:18:33,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference
[2023-06-05 06:18:34,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 06:18:34,758] [INFO] Task started: Prodigal
[2023-06-05 06:18:34,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg553a8c69-725b-4fc5-a7e4-c7f3d62263ac/GCA_934270595.1_ERR7738549_bin.11_genomic.fna.gz | prodigal -d GCA_934270595.1_ERR7738549_bin.11_genomic.fna/cds.fna -a GCA_934270595.1_ERR7738549_bin.11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 06:18:41,172] [INFO] Task succeeded: Prodigal
[2023-06-05 06:18:41,172] [INFO] Task started: HMMsearch
[2023-06-05 06:18:41,172] [INFO] Running command: hmmsearch --tblout GCA_934270595.1_ERR7738549_bin.11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference/reference_markers.hmm GCA_934270595.1_ERR7738549_bin.11_genomic.fna/protein.faa > /dev/null
[2023-06-05 06:18:41,463] [INFO] Task succeeded: HMMsearch
[2023-06-05 06:18:41,464] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg553a8c69-725b-4fc5-a7e4-c7f3d62263ac/GCA_934270595.1_ERR7738549_bin.11_genomic.fna.gz]
[2023-06-05 06:18:41,490] [INFO] Query marker FASTA was written to GCA_934270595.1_ERR7738549_bin.11_genomic.fna/markers.fasta
[2023-06-05 06:18:41,491] [INFO] Task started: Blastn
[2023-06-05 06:18:41,491] [INFO] Running command: blastn -query GCA_934270595.1_ERR7738549_bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference/reference_markers.fasta -out GCA_934270595.1_ERR7738549_bin.11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:18:41,970] [INFO] Task succeeded: Blastn
[2023-06-05 06:18:41,974] [INFO] Selected 17 target genomes.
[2023-06-05 06:18:41,975] [INFO] Target genome list was writen to GCA_934270595.1_ERR7738549_bin.11_genomic.fna/target_genomes.txt
[2023-06-05 06:18:41,977] [INFO] Task started: fastANI
[2023-06-05 06:18:41,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg553a8c69-725b-4fc5-a7e4-c7f3d62263ac/GCA_934270595.1_ERR7738549_bin.11_genomic.fna.gz --refList GCA_934270595.1_ERR7738549_bin.11_genomic.fna/target_genomes.txt --output GCA_934270595.1_ERR7738549_bin.11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 06:18:51,512] [INFO] Task succeeded: fastANI
[2023-06-05 06:18:51,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 06:18:51,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 06:18:51,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 06:18:51,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 06:18:51,515] [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
--------------------------------------------------------------------------------
[2023-06-05 06:18:51,517] [INFO] DFAST Taxonomy check result was written to GCA_934270595.1_ERR7738549_bin.11_genomic.fna/tc_result.tsv
[2023-06-05 06:18:51,518] [INFO] ===== Taxonomy check completed =====
[2023-06-05 06:18:51,518] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 06:18:51,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference/checkm_data
[2023-06-05 06:18:51,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 06:18:51,554] [INFO] Task started: CheckM
[2023-06-05 06:18:51,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934270595.1_ERR7738549_bin.11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934270595.1_ERR7738549_bin.11_genomic.fna/checkm_input GCA_934270595.1_ERR7738549_bin.11_genomic.fna/checkm_result
[2023-06-05 06:19:17,594] [INFO] Task succeeded: CheckM
[2023-06-05 06:19:17,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 06:19:17,623] [INFO] ===== Completeness check finished =====
[2023-06-05 06:19:17,623] [INFO] ===== Start GTDB Search =====
[2023-06-05 06:19:17,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934270595.1_ERR7738549_bin.11_genomic.fna/markers.fasta)
[2023-06-05 06:19:17,624] [INFO] Task started: Blastn
[2023-06-05 06:19:17,624] [INFO] Running command: blastn -query GCA_934270595.1_ERR7738549_bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg86045fb6-c54b-4ece-8647-a6d216f1741f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934270595.1_ERR7738549_bin.11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:19:18,067] [INFO] Task succeeded: Blastn
[2023-06-05 06:19:18,072] [INFO] Selected 17 target genomes.
[2023-06-05 06:19:18,072] [INFO] Target genome list was writen to GCA_934270595.1_ERR7738549_bin.11_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 06:19:18,176] [INFO] Task started: fastANI
[2023-06-05 06:19:18,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg553a8c69-725b-4fc5-a7e4-c7f3d62263ac/GCA_934270595.1_ERR7738549_bin.11_genomic.fna.gz --refList GCA_934270595.1_ERR7738549_bin.11_genomic.fna/target_genomes_gtdb.txt --output GCA_934270595.1_ERR7738549_bin.11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 06:19:26,281] [INFO] Task succeeded: fastANI
[2023-06-05 06:19:26,288] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 06:19:26,288] [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_003478935.1	s__KLE1615 sp900066985	97.2483	755	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	97.20	95.19	0.86	0.78	12	conclusive
GCA_905214365.1	s__KLE1615 sp905214365	76.6982	87	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 06:19:26,291] [INFO] GTDB search result was written to GCA_934270595.1_ERR7738549_bin.11_genomic.fna/result_gtdb.tsv
[2023-06-05 06:19:26,291] [INFO] ===== GTDB Search completed =====
[2023-06-05 06:19:26,294] [INFO] DFAST_QC result json was written to GCA_934270595.1_ERR7738549_bin.11_genomic.fna/dqc_result.json
[2023-06-05 06:19:26,294] [INFO] DFAST_QC completed!
[2023-06-05 06:19:26,295] [INFO] Total running time: 0h0m53s