[2023-06-19 12:57:44,991] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:57:45,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:57:45,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference
[2023-06-19 12:57:46,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:57:46,228] [INFO] Task started: Prodigal
[2023-06-19 12:57:46,228] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2109c4c-6f58-4dd4-a54e-c15ff80b3ef8/GCA_018902995.1_ASM1890299v1_genomic.fna.gz | prodigal -d GCA_018902995.1_ASM1890299v1_genomic.fna/cds.fna -a GCA_018902995.1_ASM1890299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:57:55,122] [INFO] Task succeeded: Prodigal
[2023-06-19 12:57:55,123] [INFO] Task started: HMMsearch
[2023-06-19 12:57:55,123] [INFO] Running command: hmmsearch --tblout GCA_018902995.1_ASM1890299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference/reference_markers.hmm GCA_018902995.1_ASM1890299v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:57:55,374] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:57:55,376] [INFO] Found 6/6 markers.
[2023-06-19 12:57:55,409] [INFO] Query marker FASTA was written to GCA_018902995.1_ASM1890299v1_genomic.fna/markers.fasta
[2023-06-19 12:57:55,410] [INFO] Task started: Blastn
[2023-06-19 12:57:55,410] [INFO] Running command: blastn -query GCA_018902995.1_ASM1890299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference/reference_markers.fasta -out GCA_018902995.1_ASM1890299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:57:56,321] [INFO] Task succeeded: Blastn
[2023-06-19 12:57:56,395] [INFO] Selected 23 target genomes.
[2023-06-19 12:57:56,396] [INFO] Target genome list was writen to GCA_018902995.1_ASM1890299v1_genomic.fna/target_genomes.txt
[2023-06-19 12:57:56,403] [INFO] Task started: fastANI
[2023-06-19 12:57:56,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2109c4c-6f58-4dd4-a54e-c15ff80b3ef8/GCA_018902995.1_ASM1890299v1_genomic.fna.gz --refList GCA_018902995.1_ASM1890299v1_genomic.fna/target_genomes.txt --output GCA_018902995.1_ASM1890299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:58:10,990] [INFO] Task succeeded: fastANI
[2023-06-19 12:58:10,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:58:10,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:58:11,014] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:58:11,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:58:11,014] [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
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	79.0677	401	960	95	below_threshold
Micropruina glycogenica		GCA_900289045.1	75385	75385	type	True	77.8525	216	960	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_004324765.1	433330	433330	type	True	77.5721	160	960	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	77.5486	163	960	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	77.5124	166	960	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.5075	184	960	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	77.3614	159	960	95	below_threshold
Propioniciclava flava	strain=VG341	GCA_004126535.1	2072026	2072026	type	True	77.3478	122	960	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.3445	186	960	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.1994	140	960	95	below_threshold
Luteococcus japonicus	strain=DSM 10546	GCA_003752415.1	33984	33984	type	True	77.1621	152	960	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.0688	178	960	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.0254	194	960	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.0088	166	960	95	below_threshold
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	76.9857	151	960	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	76.9434	152	960	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	76.8709	150	960	95	below_threshold
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	76.7449	139	960	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	76.7116	170	960	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	76.6649	165	960	95	below_threshold
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	76.485	94	960	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	75.6904	102	960	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	75.6424	115	960	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:58:11,016] [INFO] DFAST Taxonomy check result was written to GCA_018902995.1_ASM1890299v1_genomic.fna/tc_result.tsv
[2023-06-19 12:58:11,017] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:58:11,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:58:11,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference/checkm_data
[2023-06-19 12:58:11,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:58:11,052] [INFO] Task started: CheckM
[2023-06-19 12:58:11,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018902995.1_ASM1890299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018902995.1_ASM1890299v1_genomic.fna/checkm_input GCA_018902995.1_ASM1890299v1_genomic.fna/checkm_result
[2023-06-19 12:58:41,326] [INFO] Task succeeded: CheckM
[2023-06-19 12:58:41,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:58:41,348] [INFO] ===== Completeness check finished =====
[2023-06-19 12:58:41,349] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:58:41,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018902995.1_ASM1890299v1_genomic.fna/markers.fasta)
[2023-06-19 12:58:41,349] [INFO] Task started: Blastn
[2023-06-19 12:58:41,350] [INFO] Running command: blastn -query GCA_018902995.1_ASM1890299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71081e20-815c-4918-ba2e-58bc26380de2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018902995.1_ASM1890299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:58:42,662] [INFO] Task succeeded: Blastn
[2023-06-19 12:58:42,667] [INFO] Selected 11 target genomes.
[2023-06-19 12:58:42,667] [INFO] Target genome list was writen to GCA_018902995.1_ASM1890299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:58:42,674] [INFO] Task started: fastANI
[2023-06-19 12:58:42,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2109c4c-6f58-4dd4-a54e-c15ff80b3ef8/GCA_018902995.1_ASM1890299v1_genomic.fna.gz --refList GCA_018902995.1_ASM1890299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018902995.1_ASM1890299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:58:49,512] [INFO] Task succeeded: fastANI
[2023-06-19 12:58:49,523] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:58:49,524] [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_013791955.1	s__Propionicimonas sp013791955	99.8323	953	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	99.92	99.76	0.99	0.97	15	conclusive
GCA_002428365.1	s__Propionicimonas sp002428365	92.7387	778	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841335.1	s__Propionicimonas sp002841335	80.3384	572	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563675.1	s__Propionicimonas paludicola	79.0613	402	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603275.1	s__Propionicimonas sp001603275	78.9296	368	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482525.1	s__Propionicimonas sp002482525	78.7269	368	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	78.7077	332	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	78.609	387	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413345.1	s__Propionicimonas sp002413345	78.403	301	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451975.1	s__Propionicimonas sp003451975	78.2261	208	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004324755.1	s__Brevilactibacter sinopodophylli	77.3297	187	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:58:49,526] [INFO] GTDB search result was written to GCA_018902995.1_ASM1890299v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:58:49,526] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:58:49,530] [INFO] DFAST_QC result json was written to GCA_018902995.1_ASM1890299v1_genomic.fna/dqc_result.json
[2023-06-19 12:58:49,530] [INFO] DFAST_QC completed!
[2023-06-19 12:58:49,530] [INFO] Total running time: 0h1m5s