[2023-06-30 15:20:57,183] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:20:57,190] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:20:57,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference
[2023-06-30 15:20:58,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:20:58,538] [INFO] Task started: Prodigal
[2023-06-30 15:20:58,539] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3f91bcc-272e-457b-93f0-1f11b2d98332/GCA_007694885.1_ASM769488v1_genomic.fna.gz | prodigal -d GCA_007694885.1_ASM769488v1_genomic.fna/cds.fna -a GCA_007694885.1_ASM769488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:21:05,201] [INFO] Task succeeded: Prodigal
[2023-06-30 15:21:05,202] [INFO] Task started: HMMsearch
[2023-06-30 15:21:05,202] [INFO] Running command: hmmsearch --tblout GCA_007694885.1_ASM769488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference/reference_markers.hmm GCA_007694885.1_ASM769488v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:21:05,438] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:21:05,440] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf3f91bcc-272e-457b-93f0-1f11b2d98332/GCA_007694885.1_ASM769488v1_genomic.fna.gz]
[2023-06-30 15:21:05,472] [INFO] Query marker FASTA was written to GCA_007694885.1_ASM769488v1_genomic.fna/markers.fasta
[2023-06-30 15:21:05,472] [INFO] Task started: Blastn
[2023-06-30 15:21:05,472] [INFO] Running command: blastn -query GCA_007694885.1_ASM769488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference/reference_markers.fasta -out GCA_007694885.1_ASM769488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:21:06,273] [INFO] Task succeeded: Blastn
[2023-06-30 15:21:06,278] [INFO] Selected 24 target genomes.
[2023-06-30 15:21:06,279] [INFO] Target genome list was writen to GCA_007694885.1_ASM769488v1_genomic.fna/target_genomes.txt
[2023-06-30 15:21:06,282] [INFO] Task started: fastANI
[2023-06-30 15:21:06,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3f91bcc-272e-457b-93f0-1f11b2d98332/GCA_007694885.1_ASM769488v1_genomic.fna.gz --refList GCA_007694885.1_ASM769488v1_genomic.fna/target_genomes.txt --output GCA_007694885.1_ASM769488v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:21:21,234] [INFO] Task succeeded: fastANI
[2023-06-30 15:21:21,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:21:21,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:21:21,253] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:21:21,253] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:21:21,253] [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
Wenzhouxiangella marina	strain=DSM 103414	GCA_014203035.1	1579979	1579979	type	True	78.3155	288	760	95	below_threshold
Wenzhouxiangella marina	strain=KCTC 42284	GCA_001187785.1	1579979	1579979	type	True	78.2768	288	760	95	below_threshold
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	78.2515	271	760	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	76.5889	126	760	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	76.4926	139	760	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	76.3592	108	760	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.3348	124	760	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	76.3033	99	760	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.2868	123	760	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	76.2858	108	760	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.2172	76	760	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	76.1185	72	760	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	76.1165	97	760	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.1097	135	760	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.0352	90	760	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	76.0284	70	760	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.0267	50	760	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	75.9694	77	760	95	below_threshold
Xanthomonas euvesicatoria	strain=LMG 27970	GCA_001401555.1	456327	456327	type	True	75.9676	72	760	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.6532	102	760	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	75.5896	56	760	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.571	80	760	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	75.4111	59	760	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	75.1123	99	760	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:21:21,258] [INFO] DFAST Taxonomy check result was written to GCA_007694885.1_ASM769488v1_genomic.fna/tc_result.tsv
[2023-06-30 15:21:21,259] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:21:21,259] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:21:21,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference/checkm_data
[2023-06-30 15:21:21,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:21:21,293] [INFO] Task started: CheckM
[2023-06-30 15:21:21,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007694885.1_ASM769488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007694885.1_ASM769488v1_genomic.fna/checkm_input GCA_007694885.1_ASM769488v1_genomic.fna/checkm_result
[2023-06-30 15:21:46,726] [INFO] Task succeeded: CheckM
[2023-06-30 15:21:46,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:21:46,749] [INFO] ===== Completeness check finished =====
[2023-06-30 15:21:46,750] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:21:46,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007694885.1_ASM769488v1_genomic.fna/markers.fasta)
[2023-06-30 15:21:46,751] [INFO] Task started: Blastn
[2023-06-30 15:21:46,751] [INFO] Running command: blastn -query GCA_007694885.1_ASM769488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a7d8703-f296-4a6e-bd70-43338a7335f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_007694885.1_ASM769488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:21:48,168] [INFO] Task succeeded: Blastn
[2023-06-30 15:21:48,172] [INFO] Selected 11 target genomes.
[2023-06-30 15:21:48,173] [INFO] Target genome list was writen to GCA_007694885.1_ASM769488v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:21:48,178] [INFO] Task started: fastANI
[2023-06-30 15:21:48,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3f91bcc-272e-457b-93f0-1f11b2d98332/GCA_007694885.1_ASM769488v1_genomic.fna.gz --refList GCA_007694885.1_ASM769488v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007694885.1_ASM769488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:21:55,087] [INFO] Task succeeded: fastANI
[2023-06-30 15:21:55,108] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:21:55,108] [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_007694885.1	s__Wenzhouxiangella sp007694885	100.0	748	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003560975.1	s__Wenzhouxiangella sp003560975	85.8573	610	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565625.1	s__Wenzhouxiangella sp003565625	81.1925	419	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121485.1	s__Wenzhouxiangella sp007121485	80.444	263	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	99.57	99.47	0.88	0.87	3	-
GCF_010499265.1	s__Wenzhouxiangella sp010499265	80.4221	467	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135355.1	s__Wenzhouxiangella sp007135355	79.2986	305	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	99.04	98.85	0.81	0.71	3	-
GCA_007116585.1	s__Wenzhouxiangella sp007116585	78.9596	212	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	98.00	98.00	0.65	0.65	2	-
GCF_012272825.1	s__GCA-2722315 sp012272825	77.9866	255	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014725735.1	s__Wenzhouxiangella sp014725735	77.8612	256	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833355.1	s__Denitratisoma sp007833355	75.6376	65	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657635.1	s__Kinneretia sp015657635	75.1799	58	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:21:55,111] [INFO] GTDB search result was written to GCA_007694885.1_ASM769488v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:21:55,112] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:21:55,116] [INFO] DFAST_QC result json was written to GCA_007694885.1_ASM769488v1_genomic.fna/dqc_result.json
[2023-06-30 15:21:55,116] [INFO] DFAST_QC completed!
[2023-06-30 15:21:55,116] [INFO] Total running time: 0h0m58s