[2023-06-13 04:35:33,400] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:35:33,407] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:35:33,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference
[2023-06-13 04:35:34,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:35:34,586] [INFO] Task started: Prodigal
[2023-06-13 04:35:34,587] [INFO] Running command: gunzip -c /var/lib/cwl/stgd40a03ed-be35-4f64-b451-d7ba3cc44030/GCA_022826965.1_ASM2282696v1_genomic.fna.gz | prodigal -d GCA_022826965.1_ASM2282696v1_genomic.fna/cds.fna -a GCA_022826965.1_ASM2282696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:35:43,029] [INFO] Task succeeded: Prodigal
[2023-06-13 04:35:43,029] [INFO] Task started: HMMsearch
[2023-06-13 04:35:43,029] [INFO] Running command: hmmsearch --tblout GCA_022826965.1_ASM2282696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference/reference_markers.hmm GCA_022826965.1_ASM2282696v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:35:43,244] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:35:43,245] [INFO] Found 6/6 markers.
[2023-06-13 04:35:43,279] [INFO] Query marker FASTA was written to GCA_022826965.1_ASM2282696v1_genomic.fna/markers.fasta
[2023-06-13 04:35:43,280] [INFO] Task started: Blastn
[2023-06-13 04:35:43,280] [INFO] Running command: blastn -query GCA_022826965.1_ASM2282696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference/reference_markers.fasta -out GCA_022826965.1_ASM2282696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:35:43,894] [INFO] Task succeeded: Blastn
[2023-06-13 04:35:43,899] [INFO] Selected 20 target genomes.
[2023-06-13 04:35:43,899] [INFO] Target genome list was writen to GCA_022826965.1_ASM2282696v1_genomic.fna/target_genomes.txt
[2023-06-13 04:35:43,905] [INFO] Task started: fastANI
[2023-06-13 04:35:43,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgd40a03ed-be35-4f64-b451-d7ba3cc44030/GCA_022826965.1_ASM2282696v1_genomic.fna.gz --refList GCA_022826965.1_ASM2282696v1_genomic.fna/target_genomes.txt --output GCA_022826965.1_ASM2282696v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:35:58,767] [INFO] Task succeeded: fastANI
[2023-06-13 04:35:58,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:35:58,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:35:58,774] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:35:58,774] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:35:58,774] [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
Tepidiforma bonchosmolovskayae	strain=3753O	GCA_008838325.1	2601677	2601677	type	True	75.6057	57	996	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	74.9869	66	996	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	74.9016	65	996	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	74.874	63	996	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	74.5799	61	996	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:35:58,779] [INFO] DFAST Taxonomy check result was written to GCA_022826965.1_ASM2282696v1_genomic.fna/tc_result.tsv
[2023-06-13 04:35:58,779] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:35:58,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:35:58,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference/checkm_data
[2023-06-13 04:35:58,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:35:58,813] [INFO] Task started: CheckM
[2023-06-13 04:35:58,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022826965.1_ASM2282696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022826965.1_ASM2282696v1_genomic.fna/checkm_input GCA_022826965.1_ASM2282696v1_genomic.fna/checkm_result
[2023-06-13 04:36:28,224] [INFO] Task succeeded: CheckM
[2023-06-13 04:36:28,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:36:28,242] [INFO] ===== Completeness check finished =====
[2023-06-13 04:36:28,242] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:36:28,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022826965.1_ASM2282696v1_genomic.fna/markers.fasta)
[2023-06-13 04:36:28,242] [INFO] Task started: Blastn
[2023-06-13 04:36:28,243] [INFO] Running command: blastn -query GCA_022826965.1_ASM2282696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ff98eca-2ce9-49f1-90f8-db5ab8fe539d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022826965.1_ASM2282696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:29,100] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:29,104] [INFO] Selected 13 target genomes.
[2023-06-13 04:36:29,104] [INFO] Target genome list was writen to GCA_022826965.1_ASM2282696v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:36:29,115] [INFO] Task started: fastANI
[2023-06-13 04:36:29,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgd40a03ed-be35-4f64-b451-d7ba3cc44030/GCA_022826965.1_ASM2282696v1_genomic.fna.gz --refList GCA_022826965.1_ASM2282696v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022826965.1_ASM2282696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:36:35,802] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:35,808] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 04:36:35,809] [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	82.2189	686	996	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	80.8711	606	996	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	80.1756	613	996	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	79.6071	432	996	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841435.1	s__UBA2991 sp009841435	76.3215	74	996	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UBA2991	95.0	97.17	95.58	0.93	0.85	4	-
GCA_009837285.1	s__VXMT01 sp009837285	75.891	82	996	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	95.62	95.50	0.87	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-13 04:36:35,811] [INFO] GTDB search result was written to GCA_022826965.1_ASM2282696v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:36:35,811] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:36:35,814] [INFO] DFAST_QC result json was written to GCA_022826965.1_ASM2282696v1_genomic.fna/dqc_result.json
[2023-06-13 04:36:35,814] [INFO] DFAST_QC completed!
[2023-06-13 04:36:35,814] [INFO] Total running time: 0h1m2s