[2023-06-30 01:12:05,948] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:12:05,952] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:12:05,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference
[2023-06-30 01:12:07,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:12:07,391] [INFO] Task started: Prodigal
[2023-06-30 01:12:07,392] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbdd4f3f-eff2-46e3-9dc7-d9ea0f2a25d6/GCA_024683035.1_ASM2468303v1_genomic.fna.gz | prodigal -d GCA_024683035.1_ASM2468303v1_genomic.fna/cds.fna -a GCA_024683035.1_ASM2468303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:12:12,913] [INFO] Task succeeded: Prodigal
[2023-06-30 01:12:12,913] [INFO] Task started: HMMsearch
[2023-06-30 01:12:12,913] [INFO] Running command: hmmsearch --tblout GCA_024683035.1_ASM2468303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference/reference_markers.hmm GCA_024683035.1_ASM2468303v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:12:13,187] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:12:13,188] [INFO] Found 6/6 markers.
[2023-06-30 01:12:13,211] [INFO] Query marker FASTA was written to GCA_024683035.1_ASM2468303v1_genomic.fna/markers.fasta
[2023-06-30 01:12:13,211] [INFO] Task started: Blastn
[2023-06-30 01:12:13,211] [INFO] Running command: blastn -query GCA_024683035.1_ASM2468303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference/reference_markers.fasta -out GCA_024683035.1_ASM2468303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:13,912] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:13,916] [INFO] Selected 35 target genomes.
[2023-06-30 01:12:13,916] [INFO] Target genome list was writen to GCA_024683035.1_ASM2468303v1_genomic.fna/target_genomes.txt
[2023-06-30 01:12:13,919] [INFO] Task started: fastANI
[2023-06-30 01:12:13,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbdd4f3f-eff2-46e3-9dc7-d9ea0f2a25d6/GCA_024683035.1_ASM2468303v1_genomic.fna.gz --refList GCA_024683035.1_ASM2468303v1_genomic.fna/target_genomes.txt --output GCA_024683035.1_ASM2468303v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:12:40,082] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:40,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:12:40,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:12:40,085] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:12:40,085] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 01:12:40,085] [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 01:12:40,088] [INFO] DFAST Taxonomy check result was written to GCA_024683035.1_ASM2468303v1_genomic.fna/tc_result.tsv
[2023-06-30 01:12:40,088] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:12:40,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:12:40,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference/checkm_data
[2023-06-30 01:12:40,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:12:40,122] [INFO] Task started: CheckM
[2023-06-30 01:12:40,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024683035.1_ASM2468303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024683035.1_ASM2468303v1_genomic.fna/checkm_input GCA_024683035.1_ASM2468303v1_genomic.fna/checkm_result
[2023-06-30 01:13:02,775] [INFO] Task succeeded: CheckM
[2023-06-30 01:13:02,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:13:02,799] [INFO] ===== Completeness check finished =====
[2023-06-30 01:13:02,800] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:13:02,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024683035.1_ASM2468303v1_genomic.fna/markers.fasta)
[2023-06-30 01:13:02,800] [INFO] Task started: Blastn
[2023-06-30 01:13:02,801] [INFO] Running command: blastn -query GCA_024683035.1_ASM2468303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb8e8f0f-31b6-4f5b-8dc5-30118c5ed221/dqc_reference/reference_markers_gtdb.fasta -out GCA_024683035.1_ASM2468303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:13:03,612] [INFO] Task succeeded: Blastn
[2023-06-30 01:13:03,617] [INFO] Selected 36 target genomes.
[2023-06-30 01:13:03,617] [INFO] Target genome list was writen to GCA_024683035.1_ASM2468303v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:13:03,631] [INFO] Task started: fastANI
[2023-06-30 01:13:03,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbdd4f3f-eff2-46e3-9dc7-d9ea0f2a25d6/GCA_024683035.1_ASM2468303v1_genomic.fna.gz --refList GCA_024683035.1_ASM2468303v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024683035.1_ASM2468303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:13:20,082] [INFO] Task succeeded: fastANI
[2023-06-30 01:13:20,092] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 01:13:20,092] [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_902783945.1	s__Bilifractor sp902783945	78.4204	192	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795835.1	s__Bilifractor sp902795835	77.4293	61	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000702845.1	s__Bilifractor sp000702845	76.8043	54	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433615.1	s__Bilifractor sp017433615	76.4657	55	630	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 01:13:20,094] [INFO] GTDB search result was written to GCA_024683035.1_ASM2468303v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:13:20,095] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:13:20,098] [INFO] DFAST_QC result json was written to GCA_024683035.1_ASM2468303v1_genomic.fna/dqc_result.json
[2023-06-30 01:13:20,098] [INFO] DFAST_QC completed!
[2023-06-30 01:13:20,098] [INFO] Total running time: 0h1m14s