[2023-06-08 05:13:33,739] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:13:33,741] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:13:33,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference
[2023-06-08 05:13:35,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:13:35,537] [INFO] Task started: Prodigal
[2023-06-08 05:13:35,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg96c93952-2cfd-4955-9294-4344b16b544f/GCA_945861475.1_MaE-04nov19-347_genomic.fna.gz | prodigal -d GCA_945861475.1_MaE-04nov19-347_genomic.fna/cds.fna -a GCA_945861475.1_MaE-04nov19-347_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:13:38,266] [INFO] Task succeeded: Prodigal
[2023-06-08 05:13:38,266] [INFO] Task started: HMMsearch
[2023-06-08 05:13:38,267] [INFO] Running command: hmmsearch --tblout GCA_945861475.1_MaE-04nov19-347_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference/reference_markers.hmm GCA_945861475.1_MaE-04nov19-347_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:13:38,475] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:13:38,477] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg96c93952-2cfd-4955-9294-4344b16b544f/GCA_945861475.1_MaE-04nov19-347_genomic.fna.gz]
[2023-06-08 05:13:38,495] [INFO] Query marker FASTA was written to GCA_945861475.1_MaE-04nov19-347_genomic.fna/markers.fasta
[2023-06-08 05:13:38,495] [INFO] Task started: Blastn
[2023-06-08 05:13:38,495] [INFO] Running command: blastn -query GCA_945861475.1_MaE-04nov19-347_genomic.fna/markers.fasta -db /var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference/reference_markers.fasta -out GCA_945861475.1_MaE-04nov19-347_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:13:38,991] [INFO] Task succeeded: Blastn
[2023-06-08 05:13:38,996] [INFO] Selected 6 target genomes.
[2023-06-08 05:13:38,997] [INFO] Target genome list was writen to GCA_945861475.1_MaE-04nov19-347_genomic.fna/target_genomes.txt
[2023-06-08 05:13:39,000] [INFO] Task started: fastANI
[2023-06-08 05:13:39,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg96c93952-2cfd-4955-9294-4344b16b544f/GCA_945861475.1_MaE-04nov19-347_genomic.fna.gz --refList GCA_945861475.1_MaE-04nov19-347_genomic.fna/target_genomes.txt --output GCA_945861475.1_MaE-04nov19-347_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:13:43,078] [INFO] Task succeeded: fastANI
[2023-06-08 05:13:43,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:13:43,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:13:43,082] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:13:43,082] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:13:43,082] [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
--------------------------------------------------------------------------------
[2023-06-08 05:13:43,084] [INFO] DFAST Taxonomy check result was written to GCA_945861475.1_MaE-04nov19-347_genomic.fna/tc_result.tsv
[2023-06-08 05:13:43,085] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:13:43,085] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:13:43,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference/checkm_data
[2023-06-08 05:13:43,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:13:43,105] [INFO] Task started: CheckM
[2023-06-08 05:13:43,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945861475.1_MaE-04nov19-347_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945861475.1_MaE-04nov19-347_genomic.fna/checkm_input GCA_945861475.1_MaE-04nov19-347_genomic.fna/checkm_result
[2023-06-08 05:13:59,853] [INFO] Task succeeded: CheckM
[2023-06-08 05:13:59,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:13:59,874] [INFO] ===== Completeness check finished =====
[2023-06-08 05:13:59,875] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:13:59,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945861475.1_MaE-04nov19-347_genomic.fna/markers.fasta)
[2023-06-08 05:13:59,876] [INFO] Task started: Blastn
[2023-06-08 05:13:59,876] [INFO] Running command: blastn -query GCA_945861475.1_MaE-04nov19-347_genomic.fna/markers.fasta -db /var/lib/cwl/stg403f6e1c-b5ad-4a3b-bba9-0ccc77b15a10/dqc_reference/reference_markers_gtdb.fasta -out GCA_945861475.1_MaE-04nov19-347_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:00,380] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:00,385] [INFO] Selected 11 target genomes.
[2023-06-08 05:14:00,386] [INFO] Target genome list was writen to GCA_945861475.1_MaE-04nov19-347_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:14:00,391] [INFO] Task started: fastANI
[2023-06-08 05:14:00,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg96c93952-2cfd-4955-9294-4344b16b544f/GCA_945861475.1_MaE-04nov19-347_genomic.fna.gz --refList GCA_945861475.1_MaE-04nov19-347_genomic.fna/target_genomes_gtdb.txt --output GCA_945861475.1_MaE-04nov19-347_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:14:03,241] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:03,250] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:14:03,251] [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_016463105.1	s__BACL27 sp016463105	97.2928	251	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014190295.1	s__BACL27 sp014190295	92.7691	255	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737635.1	s__BACL27 sp002737635	79.3166	95	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703975.1	s__BACL27 sp009703975	79.1813	120	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	97.18	96.93	0.73	0.69	4	-
GCA_014190055.1	s__BACL27 sp014190055	78.743	83	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	95.53	95.36	0.86	0.77	8	-
GCA_016870935.1	s__BACL27 sp016870935	77.0713	54	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204455.1	s__BACL27 sp013204455	76.5732	71	300	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:14:03,253] [INFO] GTDB search result was written to GCA_945861475.1_MaE-04nov19-347_genomic.fna/result_gtdb.tsv
[2023-06-08 05:14:03,253] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:14:03,256] [INFO] DFAST_QC result json was written to GCA_945861475.1_MaE-04nov19-347_genomic.fna/dqc_result.json
[2023-06-08 05:14:03,256] [INFO] DFAST_QC completed!
[2023-06-08 05:14:03,256] [INFO] Total running time: 0h0m30s