[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference
[2024-01-24 11:05:05,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,765] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg78d92194-e345-438c-b21f-778555a75d73/GCF_026344035.1_ASM2634403v1_genomic.fna.gz | prodigal -d GCF_026344035.1_ASM2634403v1_genomic.fna/cds.fna -a GCF_026344035.1_ASM2634403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:13,854] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:13,855] [INFO] Task started: HMMsearch
[2024-01-24 11:05:13,855] [INFO] Running command: hmmsearch --tblout GCF_026344035.1_ASM2634403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference/reference_markers.hmm GCF_026344035.1_ASM2634403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:14,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:14,189] [INFO] Found 6/6 markers.
[2024-01-24 11:05:14,221] [INFO] Query marker FASTA was written to GCF_026344035.1_ASM2634403v1_genomic.fna/markers.fasta
[2024-01-24 11:05:14,222] [INFO] Task started: Blastn
[2024-01-24 11:05:14,222] [INFO] Running command: blastn -query GCF_026344035.1_ASM2634403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference/reference_markers.fasta -out GCF_026344035.1_ASM2634403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:14,865] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:14,868] [INFO] Selected 25 target genomes.
[2024-01-24 11:05:14,868] [INFO] Target genome list was writen to GCF_026344035.1_ASM2634403v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:14,876] [INFO] Task started: fastANI
[2024-01-24 11:05:14,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg78d92194-e345-438c-b21f-778555a75d73/GCF_026344035.1_ASM2634403v1_genomic.fna.gz --refList GCF_026344035.1_ASM2634403v1_genomic.fna/target_genomes.txt --output GCF_026344035.1_ASM2634403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:29,200] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:29,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:29,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:29,207] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:29,207] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:29,208] [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
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.6963	50	1177	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	77.469	128	1177	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	77.4435	130	1177	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	77.4379	127	1177	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	77.412	128	1177	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	77.3834	138	1177	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.0391	62	1177	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	76.5154	50	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:29,209] [INFO] DFAST Taxonomy check result was written to GCF_026344035.1_ASM2634403v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:29,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:29,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:29,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference/checkm_data
[2024-01-24 11:05:29,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:29,246] [INFO] Task started: CheckM
[2024-01-24 11:05:29,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344035.1_ASM2634403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344035.1_ASM2634403v1_genomic.fna/checkm_input GCF_026344035.1_ASM2634403v1_genomic.fna/checkm_result
[2024-01-24 11:05:56,657] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:56,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:56,669] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:56,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:56,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344035.1_ASM2634403v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:56,670] [INFO] Task started: Blastn
[2024-01-24 11:05:56,670] [INFO] Running command: blastn -query GCF_026344035.1_ASM2634403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg423b9049-463d-4e50-8044-858f1d24d268/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344035.1_ASM2634403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:57,752] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:57,755] [INFO] Selected 27 target genomes.
[2024-01-24 11:05:57,755] [INFO] Target genome list was writen to GCF_026344035.1_ASM2634403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:57,771] [INFO] Task started: fastANI
[2024-01-24 11:05:57,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg78d92194-e345-438c-b21f-778555a75d73/GCF_026344035.1_ASM2634403v1_genomic.fna.gz --refList GCF_026344035.1_ASM2634403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344035.1_ASM2634403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:12,612] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:12,619] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:12,619] [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
GCF_004319585.1	s__Alcaligenes faecalis_C	77.6387	126	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.23	0.95	0.93	4	-
GCF_003076515.1	s__Alcaligenes aquatilis	77.497	121	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
GCF_017377875.1	s__Alcaligenes sp017377875	77.4535	132	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002443155.1	s__Alcaligenes faecalis	77.4435	130	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_014652815.1	s__Alcaligenes pakistanensis	77.3834	138	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.08	0.97	0.96	3	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.0417	64	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCA_013416395.1	s__Pusillimonas_B sp013416395	76.8458	64	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	95.59	95.59	0.83	0.83	2	-
GCF_003971065.1	s__Candidimonas_A sp003971065	76.6359	55	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576595.1	s__Pusillimonas_A maritima	76.4259	51	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:12,620] [INFO] GTDB search result was written to GCF_026344035.1_ASM2634403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:12,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:12,623] [INFO] DFAST_QC result json was written to GCF_026344035.1_ASM2634403v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:12,623] [INFO] DFAST_QC completed!
[2024-01-24 11:06:12,623] [INFO] Total running time: 0h1m9s