[2023-06-05 01:53:58,536] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:53:58,543] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:53:58,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference
[2023-06-05 01:53:59,905] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:53:59,906] [INFO] Task started: Prodigal
[2023-06-05 01:53:59,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg936c4ddf-dba8-4bb4-9d71-e54e1addfc9c/GCA_934500585.1_ERR7738264_bin.197_genomic.fna.gz | prodigal -d GCA_934500585.1_ERR7738264_bin.197_genomic.fna/cds.fna -a GCA_934500585.1_ERR7738264_bin.197_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:54:05,871] [INFO] Task succeeded: Prodigal
[2023-06-05 01:54:05,871] [INFO] Task started: HMMsearch
[2023-06-05 01:54:05,871] [INFO] Running command: hmmsearch --tblout GCA_934500585.1_ERR7738264_bin.197_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference/reference_markers.hmm GCA_934500585.1_ERR7738264_bin.197_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:54:06,122] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:54:06,124] [INFO] Found 6/6 markers.
[2023-06-05 01:54:06,148] [INFO] Query marker FASTA was written to GCA_934500585.1_ERR7738264_bin.197_genomic.fna/markers.fasta
[2023-06-05 01:54:06,148] [INFO] Task started: Blastn
[2023-06-05 01:54:06,148] [INFO] Running command: blastn -query GCA_934500585.1_ERR7738264_bin.197_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference/reference_markers.fasta -out GCA_934500585.1_ERR7738264_bin.197_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:54:06,778] [INFO] Task succeeded: Blastn
[2023-06-05 01:54:06,783] [INFO] Selected 15 target genomes.
[2023-06-05 01:54:06,783] [INFO] Target genome list was writen to GCA_934500585.1_ERR7738264_bin.197_genomic.fna/target_genomes.txt
[2023-06-05 01:54:06,788] [INFO] Task started: fastANI
[2023-06-05 01:54:06,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg936c4ddf-dba8-4bb4-9d71-e54e1addfc9c/GCA_934500585.1_ERR7738264_bin.197_genomic.fna.gz --refList GCA_934500585.1_ERR7738264_bin.197_genomic.fna/target_genomes.txt --output GCA_934500585.1_ERR7738264_bin.197_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:54:17,098] [INFO] Task succeeded: fastANI
[2023-06-05 01:54:17,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:54:17,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:54:17,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:54:17,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:54:17,102] [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 01:54:17,104] [INFO] DFAST Taxonomy check result was written to GCA_934500585.1_ERR7738264_bin.197_genomic.fna/tc_result.tsv
[2023-06-05 01:54:17,105] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:54:17,105] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:54:17,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference/checkm_data
[2023-06-05 01:54:17,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:54:17,137] [INFO] Task started: CheckM
[2023-06-05 01:54:17,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934500585.1_ERR7738264_bin.197_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934500585.1_ERR7738264_bin.197_genomic.fna/checkm_input GCA_934500585.1_ERR7738264_bin.197_genomic.fna/checkm_result
[2023-06-05 01:54:41,881] [INFO] Task succeeded: CheckM
[2023-06-05 01:54:41,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:54:41,902] [INFO] ===== Completeness check finished =====
[2023-06-05 01:54:41,903] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:54:41,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934500585.1_ERR7738264_bin.197_genomic.fna/markers.fasta)
[2023-06-05 01:54:41,904] [INFO] Task started: Blastn
[2023-06-05 01:54:41,904] [INFO] Running command: blastn -query GCA_934500585.1_ERR7738264_bin.197_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef29ca5-1a7f-4bf7-8b8a-5cb611e2ce50/dqc_reference/reference_markers_gtdb.fasta -out GCA_934500585.1_ERR7738264_bin.197_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:54:42,941] [INFO] Task succeeded: Blastn
[2023-06-05 01:54:42,946] [INFO] Selected 28 target genomes.
[2023-06-05 01:54:42,946] [INFO] Target genome list was writen to GCA_934500585.1_ERR7738264_bin.197_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:54:43,056] [INFO] Task started: fastANI
[2023-06-05 01:54:43,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg936c4ddf-dba8-4bb4-9d71-e54e1addfc9c/GCA_934500585.1_ERR7738264_bin.197_genomic.fna.gz --refList GCA_934500585.1_ERR7738264_bin.197_genomic.fna/target_genomes_gtdb.txt --output GCA_934500585.1_ERR7738264_bin.197_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:54:54,340] [INFO] Task succeeded: fastANI
[2023-06-05 01:54:54,347] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:54:54,347] [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_008668455.1	s__RQCD01 sp008668455	97.7136	435	801	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__RQCD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015068965.1	s__RQCD01 sp015068965	77.4407	128	801	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__RQCD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:54:54,350] [INFO] GTDB search result was written to GCA_934500585.1_ERR7738264_bin.197_genomic.fna/result_gtdb.tsv
[2023-06-05 01:54:54,350] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:54:54,354] [INFO] DFAST_QC result json was written to GCA_934500585.1_ERR7738264_bin.197_genomic.fna/dqc_result.json
[2023-06-05 01:54:54,354] [INFO] DFAST_QC completed!
[2023-06-05 01:54:54,354] [INFO] Total running time: 0h0m56s