[2023-06-29 16:30:40,284] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:30:40,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:30:40,294] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference
[2023-06-29 16:30:42,047] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:30:42,048] [INFO] Task started: Prodigal
[2023-06-29 16:30:42,049] [INFO] Running command: gunzip -c /var/lib/cwl/stg11d98460-40eb-4fc8-8990-5b0244c6aff7/GCA_021152225.1_ASM2115222v1_genomic.fna.gz | prodigal -d GCA_021152225.1_ASM2115222v1_genomic.fna/cds.fna -a GCA_021152225.1_ASM2115222v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:30:44,925] [INFO] Task succeeded: Prodigal
[2023-06-29 16:30:44,926] [INFO] Task started: HMMsearch
[2023-06-29 16:30:44,926] [INFO] Running command: hmmsearch --tblout GCA_021152225.1_ASM2115222v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference/reference_markers.hmm GCA_021152225.1_ASM2115222v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:30:45,162] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:30:45,163] [INFO] Found 6/6 markers.
[2023-06-29 16:30:45,179] [INFO] Query marker FASTA was written to GCA_021152225.1_ASM2115222v1_genomic.fna/markers.fasta
[2023-06-29 16:30:45,179] [INFO] Task started: Blastn
[2023-06-29 16:30:45,179] [INFO] Running command: blastn -query GCA_021152225.1_ASM2115222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference/reference_markers.fasta -out GCA_021152225.1_ASM2115222v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:46,032] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:46,041] [INFO] Selected 19 target genomes.
[2023-06-29 16:30:46,042] [INFO] Target genome list was writen to GCA_021152225.1_ASM2115222v1_genomic.fna/target_genomes.txt
[2023-06-29 16:30:46,089] [INFO] Task started: fastANI
[2023-06-29 16:30:46,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d98460-40eb-4fc8-8990-5b0244c6aff7/GCA_021152225.1_ASM2115222v1_genomic.fna.gz --refList GCA_021152225.1_ASM2115222v1_genomic.fna/target_genomes.txt --output GCA_021152225.1_ASM2115222v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:30:56,542] [INFO] Task succeeded: fastANI
[2023-06-29 16:30:56,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:30:56,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:30:56,545] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:30:56,545] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:30:56,545] [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 16:30:56,548] [INFO] DFAST Taxonomy check result was written to GCA_021152225.1_ASM2115222v1_genomic.fna/tc_result.tsv
[2023-06-29 16:30:56,549] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:30:56,549] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:30:56,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference/checkm_data
[2023-06-29 16:30:56,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:30:56,568] [INFO] Task started: CheckM
[2023-06-29 16:30:56,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021152225.1_ASM2115222v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021152225.1_ASM2115222v1_genomic.fna/checkm_input GCA_021152225.1_ASM2115222v1_genomic.fna/checkm_result
[2023-06-29 16:31:12,986] [INFO] Task succeeded: CheckM
[2023-06-29 16:31:12,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:31:13,006] [INFO] ===== Completeness check finished =====
[2023-06-29 16:31:13,006] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:31:13,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021152225.1_ASM2115222v1_genomic.fna/markers.fasta)
[2023-06-29 16:31:13,007] [INFO] Task started: Blastn
[2023-06-29 16:31:13,007] [INFO] Running command: blastn -query GCA_021152225.1_ASM2115222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1138692-61e6-41c0-a7d4-d48cb0dbfa25/dqc_reference/reference_markers_gtdb.fasta -out GCA_021152225.1_ASM2115222v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:31:14,036] [INFO] Task succeeded: Blastn
[2023-06-29 16:31:14,041] [INFO] Selected 10 target genomes.
[2023-06-29 16:31:14,041] [INFO] Target genome list was writen to GCA_021152225.1_ASM2115222v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:31:14,045] [INFO] Task started: fastANI
[2023-06-29 16:31:14,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d98460-40eb-4fc8-8990-5b0244c6aff7/GCA_021152225.1_ASM2115222v1_genomic.fna.gz --refList GCA_021152225.1_ASM2115222v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021152225.1_ASM2115222v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:31:16,112] [INFO] Task succeeded: fastANI
[2023-06-29 16:31:16,130] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:31:16,131] [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_016301865.1	s__Enterousia sp016301865	98.0213	170	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015062495.1	s__Enterousia sp015062495	94.2051	252	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	98.28	98.17	0.95	0.93	3	-
GCA_015062525.1	s__Enterousia sp015062525	84.2309	218	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631895.1	s__Enterousia sp017631895	82.9696	170	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017383325.1	s__Enterousia sp017383325	81.5672	145	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017451625.1	s__Enterousia sp017451625	80.4602	154	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	97.00	96.52	0.94	0.93	3	-
GCA_017629245.1	s__Enterousia sp017629245	79.8428	158	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904502245.1	s__Enterousia sp904502245	79.3256	139	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017425725.1	s__Enterousia sp017425725	79.1116	84	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936185.1	s__Enterousia sp017936185	78.2061	110	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:31:16,133] [INFO] GTDB search result was written to GCA_021152225.1_ASM2115222v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:31:16,134] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:31:16,137] [INFO] DFAST_QC result json was written to GCA_021152225.1_ASM2115222v1_genomic.fna/dqc_result.json
[2023-06-29 16:31:16,137] [INFO] DFAST_QC completed!
[2023-06-29 16:31:16,137] [INFO] Total running time: 0h0m36s