[2023-06-18 21:21:03,473] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:21:03,475] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:21:03,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference
[2023-06-18 21:21:04,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:21:04,739] [INFO] Task started: Prodigal
[2023-06-18 21:21:04,739] [INFO] Running command: gunzip -c /var/lib/cwl/stga7d5d643-ff3d-4047-8449-993747821ad6/GCA_018647075.1_ASM1864707v1_genomic.fna.gz | prodigal -d GCA_018647075.1_ASM1864707v1_genomic.fna/cds.fna -a GCA_018647075.1_ASM1864707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:21:16,430] [INFO] Task succeeded: Prodigal
[2023-06-18 21:21:16,431] [INFO] Task started: HMMsearch
[2023-06-18 21:21:16,431] [INFO] Running command: hmmsearch --tblout GCA_018647075.1_ASM1864707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference/reference_markers.hmm GCA_018647075.1_ASM1864707v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:21:16,712] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:21:16,713] [INFO] Found 6/6 markers.
[2023-06-18 21:21:16,760] [INFO] Query marker FASTA was written to GCA_018647075.1_ASM1864707v1_genomic.fna/markers.fasta
[2023-06-18 21:21:16,760] [INFO] Task started: Blastn
[2023-06-18 21:21:16,760] [INFO] Running command: blastn -query GCA_018647075.1_ASM1864707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference/reference_markers.fasta -out GCA_018647075.1_ASM1864707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:21:17,478] [INFO] Task succeeded: Blastn
[2023-06-18 21:21:17,483] [INFO] Selected 30 target genomes.
[2023-06-18 21:21:17,484] [INFO] Target genome list was writen to GCA_018647075.1_ASM1864707v1_genomic.fna/target_genomes.txt
[2023-06-18 21:21:17,485] [INFO] Task started: fastANI
[2023-06-18 21:21:17,485] [INFO] Running command: fastANI --query /var/lib/cwl/stga7d5d643-ff3d-4047-8449-993747821ad6/GCA_018647075.1_ASM1864707v1_genomic.fna.gz --refList GCA_018647075.1_ASM1864707v1_genomic.fna/target_genomes.txt --output GCA_018647075.1_ASM1864707v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:21:43,250] [INFO] Task succeeded: fastANI
[2023-06-18 21:21:43,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:21:43,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:21:43,252] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:21:43,252] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:21:43,252] [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
--------------------------------------------------------------------------------
[2023-06-18 21:21:43,254] [INFO] DFAST Taxonomy check result was written to GCA_018647075.1_ASM1864707v1_genomic.fna/tc_result.tsv
[2023-06-18 21:21:43,255] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:21:43,255] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:21:43,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference/checkm_data
[2023-06-18 21:21:43,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:21:43,300] [INFO] Task started: CheckM
[2023-06-18 21:21:43,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018647075.1_ASM1864707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018647075.1_ASM1864707v1_genomic.fna/checkm_input GCA_018647075.1_ASM1864707v1_genomic.fna/checkm_result
[2023-06-18 21:22:19,681] [INFO] Task succeeded: CheckM
[2023-06-18 21:22:19,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:22:19,710] [INFO] ===== Completeness check finished =====
[2023-06-18 21:22:19,710] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:22:19,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018647075.1_ASM1864707v1_genomic.fna/markers.fasta)
[2023-06-18 21:22:19,711] [INFO] Task started: Blastn
[2023-06-18 21:22:19,711] [INFO] Running command: blastn -query GCA_018647075.1_ASM1864707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb43ea76-8485-4f1e-9b4f-88743aa26285/dqc_reference/reference_markers_gtdb.fasta -out GCA_018647075.1_ASM1864707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:22:20,572] [INFO] Task succeeded: Blastn
[2023-06-18 21:22:20,579] [INFO] Selected 16 target genomes.
[2023-06-18 21:22:20,579] [INFO] Target genome list was writen to GCA_018647075.1_ASM1864707v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:22:20,580] [INFO] Task started: fastANI
[2023-06-18 21:22:20,580] [INFO] Running command: fastANI --query /var/lib/cwl/stga7d5d643-ff3d-4047-8449-993747821ad6/GCA_018647075.1_ASM1864707v1_genomic.fna.gz --refList GCA_018647075.1_ASM1864707v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018647075.1_ASM1864707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:22:28,701] [INFO] Task succeeded: fastANI
[2023-06-18 21:22:28,715] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:22:28,715] [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_009937285.1	s__UBA1138 sp009937285	98.6538	708	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.12	98.44	0.93	0.79	16	conclusive
GCA_015664885.1	s__UBA1138 sp003447875	77.5968	147	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_009692205.1	s__UBA2982 sp009692205	76.7467	93	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390225.1	s__UBA2589 sp002390225	76.6394	90	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238865.1	s__Bin94 sp002238865	76.4936	53	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841165.1	s__Bin94 sp009841165	76.1358	51	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.63	99.39	0.93	0.90	5	-
GCA_013002885.1	s__UBA2589 sp013002885	76.0742	105	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_018678395.1	s__IDS-52 sp018678395	75.964	59	1266	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__IDS-52	95.0	98.28	98.28	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-18 21:22:28,717] [INFO] GTDB search result was written to GCA_018647075.1_ASM1864707v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:22:28,718] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:22:28,722] [INFO] DFAST_QC result json was written to GCA_018647075.1_ASM1864707v1_genomic.fna/dqc_result.json
[2023-06-18 21:22:28,723] [INFO] DFAST_QC completed!
[2023-06-18 21:22:28,723] [INFO] Total running time: 0h1m25s