[2023-06-28 10:45:53,526] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:45:53,532] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:45:53,532] [INFO] DQC Reference Directory: /var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference
[2023-06-28 10:45:54,983] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:45:54,986] [INFO] Task started: Prodigal
[2023-06-28 10:45:54,987] [INFO] Running command: gunzip -c /var/lib/cwl/stgd856fc76-af5e-4861-9d75-15a36ad0ecc9/GCA_002716705.1_ASM271670v1_genomic.fna.gz | prodigal -d GCA_002716705.1_ASM271670v1_genomic.fna/cds.fna -a GCA_002716705.1_ASM271670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:46:00,248] [INFO] Task succeeded: Prodigal
[2023-06-28 10:46:00,249] [INFO] Task started: HMMsearch
[2023-06-28 10:46:00,249] [INFO] Running command: hmmsearch --tblout GCA_002716705.1_ASM271670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference/reference_markers.hmm GCA_002716705.1_ASM271670v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:46:00,455] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:46:00,457] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd856fc76-af5e-4861-9d75-15a36ad0ecc9/GCA_002716705.1_ASM271670v1_genomic.fna.gz]
[2023-06-28 10:46:00,488] [INFO] Query marker FASTA was written to GCA_002716705.1_ASM271670v1_genomic.fna/markers.fasta
[2023-06-28 10:46:00,489] [INFO] Task started: Blastn
[2023-06-28 10:46:00,489] [INFO] Running command: blastn -query GCA_002716705.1_ASM271670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference/reference_markers.fasta -out GCA_002716705.1_ASM271670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:01,108] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:01,115] [INFO] Selected 13 target genomes.
[2023-06-28 10:46:01,116] [INFO] Target genome list was writen to GCA_002716705.1_ASM271670v1_genomic.fna/target_genomes.txt
[2023-06-28 10:46:01,116] [INFO] Task started: fastANI
[2023-06-28 10:46:01,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgd856fc76-af5e-4861-9d75-15a36ad0ecc9/GCA_002716705.1_ASM271670v1_genomic.fna.gz --refList GCA_002716705.1_ASM271670v1_genomic.fna/target_genomes.txt --output GCA_002716705.1_ASM271670v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:46:08,715] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:08,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:46:08,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:46:08,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:46:08,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:46:08,717] [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
--------------------------------------------------------------------------------
[2023-06-28 10:46:08,720] [INFO] DFAST Taxonomy check result was written to GCA_002716705.1_ASM271670v1_genomic.fna/tc_result.tsv
[2023-06-28 10:46:08,720] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:46:08,721] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:46:08,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference/checkm_data
[2023-06-28 10:46:08,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:46:08,750] [INFO] Task started: CheckM
[2023-06-28 10:46:08,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002716705.1_ASM271670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002716705.1_ASM271670v1_genomic.fna/checkm_input GCA_002716705.1_ASM271670v1_genomic.fna/checkm_result
[2023-06-28 10:46:32,390] [INFO] Task succeeded: CheckM
[2023-06-28 10:46:32,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:46:32,412] [INFO] ===== Completeness check finished =====
[2023-06-28 10:46:32,412] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:46:32,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002716705.1_ASM271670v1_genomic.fna/markers.fasta)
[2023-06-28 10:46:32,413] [INFO] Task started: Blastn
[2023-06-28 10:46:32,413] [INFO] Running command: blastn -query GCA_002716705.1_ASM271670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c9e00a-b57a-4db7-98a4-05b5af470594/dqc_reference/reference_markers_gtdb.fasta -out GCA_002716705.1_ASM271670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:33,158] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:33,163] [INFO] Selected 17 target genomes.
[2023-06-28 10:46:33,163] [INFO] Target genome list was writen to GCA_002716705.1_ASM271670v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:46:33,168] [INFO] Task started: fastANI
[2023-06-28 10:46:33,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgd856fc76-af5e-4861-9d75-15a36ad0ecc9/GCA_002716705.1_ASM271670v1_genomic.fna.gz --refList GCA_002716705.1_ASM271670v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002716705.1_ASM271670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:46:41,690] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:41,697] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:46:41,698] [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_002388005.1	s__UBA2110 sp002388005	98.0578	500	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002719335.1	s__UBA2110 sp002719335	79.8714	310	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	96.75	96.75	0.83	0.83	2	-
GCA_002705305.1	s__UBA2110 sp002705305	79.2222	306	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960315.1	s__UBA2110 sp012960315	79.0353	300	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002331465.1	s__UBA2110 sp002331465	78.7922	248	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239555.1	s__UBA2110 sp014239555	78.5411	279	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457435.1	s__MedAcidi-G3 sp002457435	77.1924	65	597	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:46:41,700] [INFO] GTDB search result was written to GCA_002716705.1_ASM271670v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:46:41,701] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:46:41,705] [INFO] DFAST_QC result json was written to GCA_002716705.1_ASM271670v1_genomic.fna/dqc_result.json
[2023-06-28 10:46:41,705] [INFO] DFAST_QC completed!
[2023-06-28 10:46:41,705] [INFO] Total running time: 0h0m48s