[2023-06-13 09:48:43,200] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:48:43,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:48:43,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference
[2023-06-13 09:48:44,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:48:44,481] [INFO] Task started: Prodigal
[2023-06-13 09:48:44,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgebc6c579-b89e-45ad-9d38-3b8e4dc76344/GCA_022820425.1_ASM2282042v1_genomic.fna.gz | prodigal -d GCA_022820425.1_ASM2282042v1_genomic.fna/cds.fna -a GCA_022820425.1_ASM2282042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:48:53,139] [INFO] Task succeeded: Prodigal
[2023-06-13 09:48:53,140] [INFO] Task started: HMMsearch
[2023-06-13 09:48:53,140] [INFO] Running command: hmmsearch --tblout GCA_022820425.1_ASM2282042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference/reference_markers.hmm GCA_022820425.1_ASM2282042v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:48:53,387] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:48:53,388] [INFO] Found 6/6 markers.
[2023-06-13 09:48:53,420] [INFO] Query marker FASTA was written to GCA_022820425.1_ASM2282042v1_genomic.fna/markers.fasta
[2023-06-13 09:48:53,421] [INFO] Task started: Blastn
[2023-06-13 09:48:53,421] [INFO] Running command: blastn -query GCA_022820425.1_ASM2282042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference/reference_markers.fasta -out GCA_022820425.1_ASM2282042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:48:54,062] [INFO] Task succeeded: Blastn
[2023-06-13 09:48:54,068] [INFO] Selected 20 target genomes.
[2023-06-13 09:48:54,068] [INFO] Target genome list was writen to GCA_022820425.1_ASM2282042v1_genomic.fna/target_genomes.txt
[2023-06-13 09:48:54,076] [INFO] Task started: fastANI
[2023-06-13 09:48:54,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc6c579-b89e-45ad-9d38-3b8e4dc76344/GCA_022820425.1_ASM2282042v1_genomic.fna.gz --refList GCA_022820425.1_ASM2282042v1_genomic.fna/target_genomes.txt --output GCA_022820425.1_ASM2282042v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:49:07,603] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:07,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:49:07,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:49:07,607] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:49:07,607] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:49:07,608] [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
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	74.8005	77	1009	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:49:07,610] [INFO] DFAST Taxonomy check result was written to GCA_022820425.1_ASM2282042v1_genomic.fna/tc_result.tsv
[2023-06-13 09:49:07,612] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:49:07,612] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:49:07,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference/checkm_data
[2023-06-13 09:49:07,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:49:07,649] [INFO] Task started: CheckM
[2023-06-13 09:49:07,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022820425.1_ASM2282042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022820425.1_ASM2282042v1_genomic.fna/checkm_input GCA_022820425.1_ASM2282042v1_genomic.fna/checkm_result
[2023-06-13 09:49:37,003] [INFO] Task succeeded: CheckM
[2023-06-13 09:49:37,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:49:37,031] [INFO] ===== Completeness check finished =====
[2023-06-13 09:49:37,032] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:49:37,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022820425.1_ASM2282042v1_genomic.fna/markers.fasta)
[2023-06-13 09:49:37,033] [INFO] Task started: Blastn
[2023-06-13 09:49:37,033] [INFO] Running command: blastn -query GCA_022820425.1_ASM2282042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33100895-e42d-4f5f-97a9-ab47b4ea74be/dqc_reference/reference_markers_gtdb.fasta -out GCA_022820425.1_ASM2282042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:37,926] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:37,933] [INFO] Selected 20 target genomes.
[2023-06-13 09:49:37,933] [INFO] Target genome list was writen to GCA_022820425.1_ASM2282042v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:49:37,944] [INFO] Task started: fastANI
[2023-06-13 09:49:37,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc6c579-b89e-45ad-9d38-3b8e4dc76344/GCA_022820425.1_ASM2282042v1_genomic.fna.gz --refList GCA_022820425.1_ASM2282042v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022820425.1_ASM2282042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:49:48,328] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:48,346] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 09:49:48,347] [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_009838735.1	s__Bin125 sp009838735	82.1676	726	1009	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	96.51	95.66	0.92	0.90	7	-
GCA_009838915.1	s__Bin125 sp009838915	81.1408	617	1009	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	98.62	97.86	0.96	0.92	7	-
GCA_002239025.1	s__Bin125 sp002239025	80.6476	676	1009	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571275.1	s__Bin125 sp007571275	79.4165	462	1009	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875695.1	s__SHYP01 sp016875695	75.7646	58	1009	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:49:48,349] [INFO] GTDB search result was written to GCA_022820425.1_ASM2282042v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:49:48,350] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:49:48,353] [INFO] DFAST_QC result json was written to GCA_022820425.1_ASM2282042v1_genomic.fna/dqc_result.json
[2023-06-13 09:49:48,354] [INFO] DFAST_QC completed!
[2023-06-13 09:49:48,354] [INFO] Total running time: 0h1m5s