[2023-06-29 21:05:36,039] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:05:36,042] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:05:36,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference
[2023-06-29 21:05:38,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:05:38,324] [INFO] Task started: Prodigal
[2023-06-29 21:05:38,325] [INFO] Running command: gunzip -c /var/lib/cwl/stga0443f45-8c74-451f-987f-c71830e72278/GCA_016708785.1_ASM1670878v1_genomic.fna.gz | prodigal -d GCA_016708785.1_ASM1670878v1_genomic.fna/cds.fna -a GCA_016708785.1_ASM1670878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:05:56,219] [INFO] Task succeeded: Prodigal
[2023-06-29 21:05:56,220] [INFO] Task started: HMMsearch
[2023-06-29 21:05:56,220] [INFO] Running command: hmmsearch --tblout GCA_016708785.1_ASM1670878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference/reference_markers.hmm GCA_016708785.1_ASM1670878v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:05:56,546] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:05:56,548] [INFO] Found 6/6 markers.
[2023-06-29 21:05:56,588] [INFO] Query marker FASTA was written to GCA_016708785.1_ASM1670878v1_genomic.fna/markers.fasta
[2023-06-29 21:05:56,589] [INFO] Task started: Blastn
[2023-06-29 21:05:56,589] [INFO] Running command: blastn -query GCA_016708785.1_ASM1670878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference/reference_markers.fasta -out GCA_016708785.1_ASM1670878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:05:57,211] [INFO] Task succeeded: Blastn
[2023-06-29 21:05:57,216] [INFO] Selected 34 target genomes.
[2023-06-29 21:05:57,217] [INFO] Target genome list was writen to GCA_016708785.1_ASM1670878v1_genomic.fna/target_genomes.txt
[2023-06-29 21:05:57,224] [INFO] Task started: fastANI
[2023-06-29 21:05:57,224] [INFO] Running command: fastANI --query /var/lib/cwl/stga0443f45-8c74-451f-987f-c71830e72278/GCA_016708785.1_ASM1670878v1_genomic.fna.gz --refList GCA_016708785.1_ASM1670878v1_genomic.fna/target_genomes.txt --output GCA_016708785.1_ASM1670878v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:06:20,671] [INFO] Task succeeded: fastANI
[2023-06-29 21:06:20,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:06:20,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:06:20,675] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:06:20,675] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:06:20,675] [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 21:06:20,677] [INFO] DFAST Taxonomy check result was written to GCA_016708785.1_ASM1670878v1_genomic.fna/tc_result.tsv
[2023-06-29 21:06:20,678] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:06:20,678] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:06:20,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference/checkm_data
[2023-06-29 21:06:20,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:06:20,740] [INFO] Task started: CheckM
[2023-06-29 21:06:20,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708785.1_ASM1670878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708785.1_ASM1670878v1_genomic.fna/checkm_input GCA_016708785.1_ASM1670878v1_genomic.fna/checkm_result
[2023-06-29 21:07:16,241] [INFO] Task succeeded: CheckM
[2023-06-29 21:07:16,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:07:16,263] [INFO] ===== Completeness check finished =====
[2023-06-29 21:07:16,263] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:07:16,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708785.1_ASM1670878v1_genomic.fna/markers.fasta)
[2023-06-29 21:07:16,264] [INFO] Task started: Blastn
[2023-06-29 21:07:16,264] [INFO] Running command: blastn -query GCA_016708785.1_ASM1670878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbf5ca0d-eb96-4712-8020-6bb4ffd60727/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708785.1_ASM1670878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:07:17,139] [INFO] Task succeeded: Blastn
[2023-06-29 21:07:17,145] [INFO] Selected 20 target genomes.
[2023-06-29 21:07:17,145] [INFO] Target genome list was writen to GCA_016708785.1_ASM1670878v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:07:17,165] [INFO] Task started: fastANI
[2023-06-29 21:07:17,165] [INFO] Running command: fastANI --query /var/lib/cwl/stga0443f45-8c74-451f-987f-c71830e72278/GCA_016708785.1_ASM1670878v1_genomic.fna.gz --refList GCA_016708785.1_ASM1670878v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708785.1_ASM1670878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:07:30,395] [INFO] Task succeeded: fastANI
[2023-06-29 21:07:30,407] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:07:30,407] [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_016708785.1	s__JADKIH01 sp016708785	100.0	1449	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKIH01	95.0	98.36	97.78	0.88	0.84	5	conclusive
GCA_016711505.1	s__JADKIH01 sp016711505	80.4095	689	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKIH01	95.0	98.77	98.54	0.94	0.91	6	-
GCA_016721305.1	s__JADKIH01 sp016721305	77.1171	196	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720935.1	s__JADKJP01 sp016720935	76.9876	98	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKJP01	95.0	99.14	99.10	0.95	0.94	3	-
GCA_016720655.1	s__JADKJP01 sp016720655	76.6043	109	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKJP01	95.0	98.44	98.22	0.95	0.93	7	-
GCA_004295015.1	s__QQVM01 sp004295015	76.2771	87	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__QQVM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:07:30,409] [INFO] GTDB search result was written to GCA_016708785.1_ASM1670878v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:07:30,410] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:07:30,413] [INFO] DFAST_QC result json was written to GCA_016708785.1_ASM1670878v1_genomic.fna/dqc_result.json
[2023-06-29 21:07:30,413] [INFO] DFAST_QC completed!
[2023-06-29 21:07:30,413] [INFO] Total running time: 0h1m54s