[2023-06-30 19:47:32,157] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:47:32,160] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:47:32,160] [INFO] DQC Reference Directory: /var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference
[2023-06-30 19:47:34,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:47:34,264] [INFO] Task started: Prodigal
[2023-06-30 19:47:34,264] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf58402b-90d6-4106-8a9d-5d30a65098e3/GCA_025992465.1_ASM2599246v1_genomic.fna.gz | prodigal -d GCA_025992465.1_ASM2599246v1_genomic.fna/cds.fna -a GCA_025992465.1_ASM2599246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:47:37,498] [INFO] Task succeeded: Prodigal
[2023-06-30 19:47:37,499] [INFO] Task started: HMMsearch
[2023-06-30 19:47:37,499] [INFO] Running command: hmmsearch --tblout GCA_025992465.1_ASM2599246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference/reference_markers.hmm GCA_025992465.1_ASM2599246v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:47:37,802] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:47:37,804] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgaf58402b-90d6-4106-8a9d-5d30a65098e3/GCA_025992465.1_ASM2599246v1_genomic.fna.gz]
[2023-06-30 19:47:37,823] [INFO] Query marker FASTA was written to GCA_025992465.1_ASM2599246v1_genomic.fna/markers.fasta
[2023-06-30 19:47:37,823] [INFO] Task started: Blastn
[2023-06-30 19:47:37,823] [INFO] Running command: blastn -query GCA_025992465.1_ASM2599246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference/reference_markers.fasta -out GCA_025992465.1_ASM2599246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:47:40,036] [INFO] Task succeeded: Blastn
[2023-06-30 19:47:40,040] [INFO] Selected 6 target genomes.
[2023-06-30 19:47:40,040] [INFO] Target genome list was writen to GCA_025992465.1_ASM2599246v1_genomic.fna/target_genomes.txt
[2023-06-30 19:47:40,041] [INFO] Task started: fastANI
[2023-06-30 19:47:40,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf58402b-90d6-4106-8a9d-5d30a65098e3/GCA_025992465.1_ASM2599246v1_genomic.fna.gz --refList GCA_025992465.1_ASM2599246v1_genomic.fna/target_genomes.txt --output GCA_025992465.1_ASM2599246v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:47:42,607] [INFO] Task succeeded: fastANI
[2023-06-30 19:47:42,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:47:42,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:47:42,616] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 19:47:42,616] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 19:47:42,617] [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
Methanobrevibacter smithii	strain=ATCC 35061; PS; DSMZ 861	GCA_000016525.1	2173	2173	type	True	97.9602	555	597	95	conclusive
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	80.284	271	597	95	below_threshold
Methanobrevibacter oralis	strain=DSM 7256	GCA_001639275.1	66851	66851	type	True	79.8555	274	597	95	below_threshold
Methanobrevibacter gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	79.5855	269	597	95	below_threshold
Methanobrevibacter arboriphilus	strain=DH1	GCA_002072215.1	39441	39441	type	True	76.8689	105	597	95	below_threshold
Methanobrevibacter cuticularis	strain=DSM 11139	GCA_001639285.1	47311	47311	type	True	76.7308	99	597	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:47:42,619] [INFO] DFAST Taxonomy check result was written to GCA_025992465.1_ASM2599246v1_genomic.fna/tc_result.tsv
[2023-06-30 19:47:42,620] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:47:42,620] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:47:42,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference/checkm_data
[2023-06-30 19:47:42,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:47:42,646] [INFO] Task started: CheckM
[2023-06-30 19:47:42,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025992465.1_ASM2599246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025992465.1_ASM2599246v1_genomic.fna/checkm_input GCA_025992465.1_ASM2599246v1_genomic.fna/checkm_result
[2023-06-30 19:48:00,433] [INFO] Task succeeded: CheckM
[2023-06-30 19:48:00,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:48:00,453] [INFO] ===== Completeness check finished =====
[2023-06-30 19:48:00,453] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:48:00,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025992465.1_ASM2599246v1_genomic.fna/markers.fasta)
[2023-06-30 19:48:00,454] [INFO] Task started: Blastn
[2023-06-30 19:48:00,454] [INFO] Running command: blastn -query GCA_025992465.1_ASM2599246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99d6492f-04a3-47aa-886b-976ac2b0e25d/dqc_reference/reference_markers_gtdb.fasta -out GCA_025992465.1_ASM2599246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:48:00,986] [INFO] Task succeeded: Blastn
[2023-06-30 19:48:00,990] [INFO] Selected 8 target genomes.
[2023-06-30 19:48:00,991] [INFO] Target genome list was writen to GCA_025992465.1_ASM2599246v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:48:00,992] [INFO] Task started: fastANI
[2023-06-30 19:48:00,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf58402b-90d6-4106-8a9d-5d30a65098e3/GCA_025992465.1_ASM2599246v1_genomic.fna.gz --refList GCA_025992465.1_ASM2599246v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025992465.1_ASM2599246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:48:04,543] [INFO] Task succeeded: fastANI
[2023-06-30 19:48:04,560] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:48:04,560] [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_000016525.1	s__Methanobrevibacter_A smithii	97.9602	555	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.32	97.88	0.94	0.83	24	conclusive
GCF_002252585.1	s__Methanobrevibacter_A smithii_A	93.1327	543	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.86	98.61	0.93	0.90	16	-
GCF_003111605.1	s__Methanobrevibacter_A woesei	80.2994	271	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	96.82	96.82	0.93	0.93	2	-
GCF_001639275.1	s__Methanobrevibacter_A oralis	79.8555	274	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.88	99.83	0.98	0.97	4	-
GCF_003814835.1	s__Methanobrevibacter_A gottschalkii	79.5667	270	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.46	98.93	0.95	0.91	3	-
GCA_900317865.1	s__Methanobrevibacter_A sp900317865	79.0669	232	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.42	95.98	0.84	0.76	8	-
GCA_017460025.1	s__Methanobrevibacter_A sp017460025	79.0248	183	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783085.1	s__Methanobrevibacter_A sp902783085	78.3101	214	597	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:48:04,562] [INFO] GTDB search result was written to GCA_025992465.1_ASM2599246v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:48:04,563] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:48:04,567] [INFO] DFAST_QC result json was written to GCA_025992465.1_ASM2599246v1_genomic.fna/dqc_result.json
[2023-06-30 19:48:04,567] [INFO] DFAST_QC completed!
[2023-06-30 19:48:04,567] [INFO] Total running time: 0h0m32s