[2023-06-13 09:14:08,642] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:14:08,644] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:14:08,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference
[2023-06-13 09:14:09,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:14:09,851] [INFO] Task started: Prodigal
[2023-06-13 09:14:09,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg16eb8bb5-6c0f-4445-9330-13f931533e0d/GCA_022425305.1_ASM2242530v1_genomic.fna.gz | prodigal -d GCA_022425305.1_ASM2242530v1_genomic.fna/cds.fna -a GCA_022425305.1_ASM2242530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:14:18,526] [INFO] Task succeeded: Prodigal
[2023-06-13 09:14:18,527] [INFO] Task started: HMMsearch
[2023-06-13 09:14:18,527] [INFO] Running command: hmmsearch --tblout GCA_022425305.1_ASM2242530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference/reference_markers.hmm GCA_022425305.1_ASM2242530v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:14:18,764] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:14:18,766] [INFO] Found 6/6 markers.
[2023-06-13 09:14:18,790] [INFO] Query marker FASTA was written to GCA_022425305.1_ASM2242530v1_genomic.fna/markers.fasta
[2023-06-13 09:14:18,790] [INFO] Task started: Blastn
[2023-06-13 09:14:18,790] [INFO] Running command: blastn -query GCA_022425305.1_ASM2242530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference/reference_markers.fasta -out GCA_022425305.1_ASM2242530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:14:19,368] [INFO] Task succeeded: Blastn
[2023-06-13 09:14:19,374] [INFO] Selected 30 target genomes.
[2023-06-13 09:14:19,374] [INFO] Target genome list was writen to GCA_022425305.1_ASM2242530v1_genomic.fna/target_genomes.txt
[2023-06-13 09:14:19,380] [INFO] Task started: fastANI
[2023-06-13 09:14:19,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg16eb8bb5-6c0f-4445-9330-13f931533e0d/GCA_022425305.1_ASM2242530v1_genomic.fna.gz --refList GCA_022425305.1_ASM2242530v1_genomic.fna/target_genomes.txt --output GCA_022425305.1_ASM2242530v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:14:34,044] [INFO] Task succeeded: fastANI
[2023-06-13 09:14:34,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:14:34,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:14:34,047] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:14:34,047] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 09:14:34,048] [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
--------------------------------------------------------------------------------
[2023-06-13 09:14:34,062] [INFO] DFAST Taxonomy check result was written to GCA_022425305.1_ASM2242530v1_genomic.fna/tc_result.tsv
[2023-06-13 09:14:34,063] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:14:34,063] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:14:34,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference/checkm_data
[2023-06-13 09:14:34,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:14:34,100] [INFO] Task started: CheckM
[2023-06-13 09:14:34,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425305.1_ASM2242530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425305.1_ASM2242530v1_genomic.fna/checkm_input GCA_022425305.1_ASM2242530v1_genomic.fna/checkm_result
[2023-06-13 09:15:04,913] [INFO] Task succeeded: CheckM
[2023-06-13 09:15:04,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 09:15:04,941] [INFO] ===== Completeness check finished =====
[2023-06-13 09:15:04,941] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:15:04,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425305.1_ASM2242530v1_genomic.fna/markers.fasta)
[2023-06-13 09:15:04,942] [INFO] Task started: Blastn
[2023-06-13 09:15:04,942] [INFO] Running command: blastn -query GCA_022425305.1_ASM2242530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f4a142f-26bf-41f5-b4ac-ba72215246be/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425305.1_ASM2242530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:15:05,712] [INFO] Task succeeded: Blastn
[2023-06-13 09:15:05,718] [INFO] Selected 16 target genomes.
[2023-06-13 09:15:05,718] [INFO] Target genome list was writen to GCA_022425305.1_ASM2242530v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:15:05,749] [INFO] Task started: fastANI
[2023-06-13 09:15:05,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg16eb8bb5-6c0f-4445-9330-13f931533e0d/GCA_022425305.1_ASM2242530v1_genomic.fna.gz --refList GCA_022425305.1_ASM2242530v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425305.1_ASM2242530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:15:11,871] [INFO] Task succeeded: fastANI
[2023-06-13 09:15:11,891] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:15:11,892] [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_018647605.1	s__UBA8316 sp018647605	97.5421	398	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009936675.1	s__UBA8316 sp009936675	81.0722	267	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002390455.1	s__UBA8316 sp002390455	79.6335	288	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_018623955.1	s__UBA8316 sp018623955	79.3986	156	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364535.1	s__UBA8316 sp002364535	78.9764	300	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002711215.1	s__UBA8316 sp002711215	78.2695	204	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
GCA_902619315.1	s__UBA8316 sp902619315	78.0785	156	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687665.1	s__UBA8316 sp002687665	78.0093	157	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336305.1	s__UBA8316 sp002336305	77.5972	191	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538555.1	s__UBA8316 sp003538555	77.1636	116	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-13 09:15:11,906] [INFO] GTDB search result was written to GCA_022425305.1_ASM2242530v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:15:11,907] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:15:11,911] [INFO] DFAST_QC result json was written to GCA_022425305.1_ASM2242530v1_genomic.fna/dqc_result.json
[2023-06-13 09:15:11,911] [INFO] DFAST_QC completed!
[2023-06-13 09:15:11,911] [INFO] Total running time: 0h1m3s