[2023-06-05 07:37:19,769] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:37:19,772] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:37:19,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference
[2023-06-05 07:37:22,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:37:22,915] [INFO] Task started: Prodigal
[2023-06-05 07:37:22,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg476e37c1-78ed-45b4-acc2-057bcec4f01f/GCA_934249265.1_ERR7738240_bin.178_genomic.fna.gz | prodigal -d GCA_934249265.1_ERR7738240_bin.178_genomic.fna/cds.fna -a GCA_934249265.1_ERR7738240_bin.178_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:37:27,692] [INFO] Task succeeded: Prodigal
[2023-06-05 07:37:27,693] [INFO] Task started: HMMsearch
[2023-06-05 07:37:27,693] [INFO] Running command: hmmsearch --tblout GCA_934249265.1_ERR7738240_bin.178_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference/reference_markers.hmm GCA_934249265.1_ERR7738240_bin.178_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:37:28,050] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:37:28,051] [INFO] Found 6/6 markers.
[2023-06-05 07:37:28,089] [INFO] Query marker FASTA was written to GCA_934249265.1_ERR7738240_bin.178_genomic.fna/markers.fasta
[2023-06-05 07:37:28,089] [INFO] Task started: Blastn
[2023-06-05 07:37:28,089] [INFO] Running command: blastn -query GCA_934249265.1_ERR7738240_bin.178_genomic.fna/markers.fasta -db /var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference/reference_markers.fasta -out GCA_934249265.1_ERR7738240_bin.178_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:37:29,621] [INFO] Task succeeded: Blastn
[2023-06-05 07:37:29,625] [INFO] Selected 21 target genomes.
[2023-06-05 07:37:29,625] [INFO] Target genome list was writen to GCA_934249265.1_ERR7738240_bin.178_genomic.fna/target_genomes.txt
[2023-06-05 07:37:29,630] [INFO] Task started: fastANI
[2023-06-05 07:37:29,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg476e37c1-78ed-45b4-acc2-057bcec4f01f/GCA_934249265.1_ERR7738240_bin.178_genomic.fna.gz --refList GCA_934249265.1_ERR7738240_bin.178_genomic.fna/target_genomes.txt --output GCA_934249265.1_ERR7738240_bin.178_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:37:39,005] [INFO] Task succeeded: fastANI
[2023-06-05 07:37:39,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:37:39,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:37:39,008] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:37:39,008] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 07:37:39,008] [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 07:37:39,010] [INFO] DFAST Taxonomy check result was written to GCA_934249265.1_ERR7738240_bin.178_genomic.fna/tc_result.tsv
[2023-06-05 07:37:39,010] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:37:39,011] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:37:39,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference/checkm_data
[2023-06-05 07:37:39,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:37:39,043] [INFO] Task started: CheckM
[2023-06-05 07:37:39,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934249265.1_ERR7738240_bin.178_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934249265.1_ERR7738240_bin.178_genomic.fna/checkm_input GCA_934249265.1_ERR7738240_bin.178_genomic.fna/checkm_result
[2023-06-05 07:37:59,691] [INFO] Task succeeded: CheckM
[2023-06-05 07:37:59,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:37:59,714] [INFO] ===== Completeness check finished =====
[2023-06-05 07:37:59,715] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:37:59,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934249265.1_ERR7738240_bin.178_genomic.fna/markers.fasta)
[2023-06-05 07:37:59,716] [INFO] Task started: Blastn
[2023-06-05 07:37:59,716] [INFO] Running command: blastn -query GCA_934249265.1_ERR7738240_bin.178_genomic.fna/markers.fasta -db /var/lib/cwl/stg84fabc24-1d73-451a-b76c-c7ebff1efcf1/dqc_reference/reference_markers_gtdb.fasta -out GCA_934249265.1_ERR7738240_bin.178_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:38:00,515] [INFO] Task succeeded: Blastn
[2023-06-05 07:38:00,519] [INFO] Selected 28 target genomes.
[2023-06-05 07:38:00,520] [INFO] Target genome list was writen to GCA_934249265.1_ERR7738240_bin.178_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:38:00,619] [INFO] Task started: fastANI
[2023-06-05 07:38:00,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg476e37c1-78ed-45b4-acc2-057bcec4f01f/GCA_934249265.1_ERR7738240_bin.178_genomic.fna.gz --refList GCA_934249265.1_ERR7738240_bin.178_genomic.fna/target_genomes_gtdb.txt --output GCA_934249265.1_ERR7738240_bin.178_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:38:08,238] [INFO] Task succeeded: fastANI
[2023-06-05 07:38:08,242] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 07:38:08,242] [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_900767815.1	s__UBA10281 sp900767815	78.3075	58	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	96.63	96.03	0.81	0.74	3	-
GCA_017453045.1	s__UBA10281 sp017453045	76.588	53	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:38:08,244] [INFO] GTDB search result was written to GCA_934249265.1_ERR7738240_bin.178_genomic.fna/result_gtdb.tsv
[2023-06-05 07:38:08,245] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:38:08,247] [INFO] DFAST_QC result json was written to GCA_934249265.1_ERR7738240_bin.178_genomic.fna/dqc_result.json
[2023-06-05 07:38:08,247] [INFO] DFAST_QC completed!
[2023-06-05 07:38:08,247] [INFO] Total running time: 0h0m48s