[2023-06-27 04:40:51,902] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:40:51,913] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:40:51,913] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference
[2023-06-27 04:40:54,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:40:54,902] [INFO] Task started: Prodigal
[2023-06-27 04:40:54,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ed5b545-67ee-4956-be4b-e942b643a155/GCA_002721175.1_ASM272117v1_genomic.fna.gz | prodigal -d GCA_002721175.1_ASM272117v1_genomic.fna/cds.fna -a GCA_002721175.1_ASM272117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:41:00,197] [INFO] Task succeeded: Prodigal
[2023-06-27 04:41:00,197] [INFO] Task started: HMMsearch
[2023-06-27 04:41:00,197] [INFO] Running command: hmmsearch --tblout GCA_002721175.1_ASM272117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference/reference_markers.hmm GCA_002721175.1_ASM272117v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:41:00,391] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:41:00,393] [INFO] Found 6/6 markers.
[2023-06-27 04:41:00,414] [INFO] Query marker FASTA was written to GCA_002721175.1_ASM272117v1_genomic.fna/markers.fasta
[2023-06-27 04:41:00,414] [INFO] Task started: Blastn
[2023-06-27 04:41:00,415] [INFO] Running command: blastn -query GCA_002721175.1_ASM272117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference/reference_markers.fasta -out GCA_002721175.1_ASM272117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:00,989] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:01,009] [INFO] Selected 30 target genomes.
[2023-06-27 04:41:01,009] [INFO] Target genome list was writen to GCA_002721175.1_ASM272117v1_genomic.fna/target_genomes.txt
[2023-06-27 04:41:01,040] [INFO] Task started: fastANI
[2023-06-27 04:41:01,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ed5b545-67ee-4956-be4b-e942b643a155/GCA_002721175.1_ASM272117v1_genomic.fna.gz --refList GCA_002721175.1_ASM272117v1_genomic.fna/target_genomes.txt --output GCA_002721175.1_ASM272117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:41:20,279] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:20,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:41:20,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:41:20,284] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:41:20,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 04:41:20,285] [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
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	75.9405	53	542	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 04:41:20,287] [INFO] DFAST Taxonomy check result was written to GCA_002721175.1_ASM272117v1_genomic.fna/tc_result.tsv
[2023-06-27 04:41:20,287] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:41:20,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:41:20,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference/checkm_data
[2023-06-27 04:41:20,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:41:20,318] [INFO] Task started: CheckM
[2023-06-27 04:41:20,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002721175.1_ASM272117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002721175.1_ASM272117v1_genomic.fna/checkm_input GCA_002721175.1_ASM272117v1_genomic.fna/checkm_result
[2023-06-27 04:41:41,360] [INFO] Task succeeded: CheckM
[2023-06-27 04:41:41,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:41:41,379] [INFO] ===== Completeness check finished =====
[2023-06-27 04:41:41,379] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:41:41,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002721175.1_ASM272117v1_genomic.fna/markers.fasta)
[2023-06-27 04:41:41,380] [INFO] Task started: Blastn
[2023-06-27 04:41:41,380] [INFO] Running command: blastn -query GCA_002721175.1_ASM272117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e3e9a5-baef-436d-b3b7-444796ef74ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_002721175.1_ASM272117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:42,197] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:42,218] [INFO] Selected 28 target genomes.
[2023-06-27 04:41:42,219] [INFO] Target genome list was writen to GCA_002721175.1_ASM272117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:41:42,232] [INFO] Task started: fastANI
[2023-06-27 04:41:42,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ed5b545-67ee-4956-be4b-e942b643a155/GCA_002721175.1_ASM272117v1_genomic.fna.gz --refList GCA_002721175.1_ASM272117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002721175.1_ASM272117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:41:55,373] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:55,379] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:41:55,379] [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_002721175.1	s__SP29 sp002721175	100.0	540	542	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SP29	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001735715.1	s__GCA001735715 sp001735715	76.8383	75	542	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_002684355.1	s__UBA3537 sp002684355	76.7612	74	542	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002690085.1	s__UBA3537 sp002690085	76.6591	64	542	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516685.1	s__UBA3537 sp902516685	76.3823	71	542	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:41:55,380] [INFO] GTDB search result was written to GCA_002721175.1_ASM272117v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:41:55,381] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:41:55,383] [INFO] DFAST_QC result json was written to GCA_002721175.1_ASM272117v1_genomic.fna/dqc_result.json
[2023-06-27 04:41:55,383] [INFO] DFAST_QC completed!
[2023-06-27 04:41:55,383] [INFO] Total running time: 0h1m3s