[2023-06-29 17:18:52,642] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:18:52,645] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:18:52,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference
[2023-06-29 17:18:54,234] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:18:54,235] [INFO] Task started: Prodigal
[2023-06-29 17:18:54,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a7da84c-f6a2-444a-b9c8-fc1a226f608e/GCA_021647685.1_ASM2164768v1_genomic.fna.gz | prodigal -d GCA_021647685.1_ASM2164768v1_genomic.fna/cds.fna -a GCA_021647685.1_ASM2164768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:19:08,349] [INFO] Task succeeded: Prodigal
[2023-06-29 17:19:08,350] [INFO] Task started: HMMsearch
[2023-06-29 17:19:08,350] [INFO] Running command: hmmsearch --tblout GCA_021647685.1_ASM2164768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference/reference_markers.hmm GCA_021647685.1_ASM2164768v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:19:08,688] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:19:08,690] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8a7da84c-f6a2-444a-b9c8-fc1a226f608e/GCA_021647685.1_ASM2164768v1_genomic.fna.gz]
[2023-06-29 17:19:08,732] [INFO] Query marker FASTA was written to GCA_021647685.1_ASM2164768v1_genomic.fna/markers.fasta
[2023-06-29 17:19:08,733] [INFO] Task started: Blastn
[2023-06-29 17:19:08,733] [INFO] Running command: blastn -query GCA_021647685.1_ASM2164768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference/reference_markers.fasta -out GCA_021647685.1_ASM2164768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:19:09,409] [INFO] Task succeeded: Blastn
[2023-06-29 17:19:09,413] [INFO] Selected 26 target genomes.
[2023-06-29 17:19:09,414] [INFO] Target genome list was writen to GCA_021647685.1_ASM2164768v1_genomic.fna/target_genomes.txt
[2023-06-29 17:19:09,416] [INFO] Task started: fastANI
[2023-06-29 17:19:09,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a7da84c-f6a2-444a-b9c8-fc1a226f608e/GCA_021647685.1_ASM2164768v1_genomic.fna.gz --refList GCA_021647685.1_ASM2164768v1_genomic.fna/target_genomes.txt --output GCA_021647685.1_ASM2164768v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:19:29,389] [INFO] Task succeeded: fastANI
[2023-06-29 17:19:29,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:19:29,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:19:29,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:19:29,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 17:19:29,395] [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
--------------------------------------------------------------------------------
[2023-06-29 17:19:29,398] [INFO] DFAST Taxonomy check result was written to GCA_021647685.1_ASM2164768v1_genomic.fna/tc_result.tsv
[2023-06-29 17:19:29,398] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:19:29,399] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:19:29,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference/checkm_data
[2023-06-29 17:19:29,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:19:29,452] [INFO] Task started: CheckM
[2023-06-29 17:19:29,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021647685.1_ASM2164768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021647685.1_ASM2164768v1_genomic.fna/checkm_input GCA_021647685.1_ASM2164768v1_genomic.fna/checkm_result
[2023-06-29 17:20:12,051] [INFO] Task succeeded: CheckM
[2023-06-29 17:20:12,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:20:12,076] [INFO] ===== Completeness check finished =====
[2023-06-29 17:20:12,076] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:20:12,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021647685.1_ASM2164768v1_genomic.fna/markers.fasta)
[2023-06-29 17:20:12,077] [INFO] Task started: Blastn
[2023-06-29 17:20:12,077] [INFO] Running command: blastn -query GCA_021647685.1_ASM2164768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40dc30ce-4335-4cd4-8e84-1ab5be92efac/dqc_reference/reference_markers_gtdb.fasta -out GCA_021647685.1_ASM2164768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:20:12,993] [INFO] Task succeeded: Blastn
[2023-06-29 17:20:12,998] [INFO] Selected 27 target genomes.
[2023-06-29 17:20:12,999] [INFO] Target genome list was writen to GCA_021647685.1_ASM2164768v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:20:13,009] [INFO] Task started: fastANI
[2023-06-29 17:20:13,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a7da84c-f6a2-444a-b9c8-fc1a226f608e/GCA_021647685.1_ASM2164768v1_genomic.fna.gz --refList GCA_021647685.1_ASM2164768v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021647685.1_ASM2164768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:20:28,478] [INFO] Task succeeded: fastANI
[2023-06-29 17:20:28,488] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 17:20:28,488] [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_002084525.1	s__NBLH01 sp002084525	75.8222	90	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__NBLH01;g__NBLH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937695.1	s__NBLH01 sp016937695	75.6373	135	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__NBLH01;g__NBLH01	95.0	99.88	99.88	0.90	0.90	2	-
GCA_015222055.1	s__B39-G9 sp015222055	74.9609	66	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__B39-G9;g__B39-G9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768155.1	s__GWA2-31-9 sp001768155	74.8891	50	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-33-38;g__GWA2-31-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:20:28,514] [INFO] GTDB search result was written to GCA_021647685.1_ASM2164768v1_genomic.fna/result_gtdb.tsv
[2023-06-29 17:20:28,515] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:20:28,518] [INFO] DFAST_QC result json was written to GCA_021647685.1_ASM2164768v1_genomic.fna/dqc_result.json
[2023-06-29 17:20:28,518] [INFO] DFAST_QC completed!
[2023-06-29 17:20:28,518] [INFO] Total running time: 0h1m36s