[2023-06-30 19:04:47,471] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:04:47,475] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:04:47,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference
[2023-06-30 19:04:49,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:04:49,115] [INFO] Task started: Prodigal
[2023-06-30 19:04:49,116] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a6a26cf-4de8-40e9-8152-717d7e38f690/GCA_025993695.1_ASM2599369v1_genomic.fna.gz | prodigal -d GCA_025993695.1_ASM2599369v1_genomic.fna/cds.fna -a GCA_025993695.1_ASM2599369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:04:56,087] [INFO] Task succeeded: Prodigal
[2023-06-30 19:04:56,088] [INFO] Task started: HMMsearch
[2023-06-30 19:04:56,088] [INFO] Running command: hmmsearch --tblout GCA_025993695.1_ASM2599369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference/reference_markers.hmm GCA_025993695.1_ASM2599369v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:04:56,344] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:04:56,345] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a6a26cf-4de8-40e9-8152-717d7e38f690/GCA_025993695.1_ASM2599369v1_genomic.fna.gz]
[2023-06-30 19:04:56,409] [INFO] Query marker FASTA was written to GCA_025993695.1_ASM2599369v1_genomic.fna/markers.fasta
[2023-06-30 19:04:56,410] [INFO] Task started: Blastn
[2023-06-30 19:04:56,410] [INFO] Running command: blastn -query GCA_025993695.1_ASM2599369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference/reference_markers.fasta -out GCA_025993695.1_ASM2599369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:04:57,216] [INFO] Task succeeded: Blastn
[2023-06-30 19:04:57,220] [INFO] Selected 29 target genomes.
[2023-06-30 19:04:57,221] [INFO] Target genome list was writen to GCA_025993695.1_ASM2599369v1_genomic.fna/target_genomes.txt
[2023-06-30 19:04:57,224] [INFO] Task started: fastANI
[2023-06-30 19:04:57,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6a26cf-4de8-40e9-8152-717d7e38f690/GCA_025993695.1_ASM2599369v1_genomic.fna.gz --refList GCA_025993695.1_ASM2599369v1_genomic.fna/target_genomes.txt --output GCA_025993695.1_ASM2599369v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:05:21,207] [INFO] Task succeeded: fastANI
[2023-06-30 19:05:21,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:05:21,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:05:21,233] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:05:21,233] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:05:21,234] [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
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	77.0695	216	636	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	77.0645	215	636	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.0581	150	636	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	77.0387	234	636	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	77.0086	145	636	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	76.9961	230	636	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.993	148	636	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.8655	193	636	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.8428	181	636	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	76.77	240	636	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	76.7222	251	636	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	76.657	167	636	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	76.6126	178	636	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	76.6075	213	636	95	below_threshold
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	76.6035	119	636	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	76.5514	208	636	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.5341	227	636	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	76.5279	206	636	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	76.5232	238	636	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	76.4911	171	636	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	76.4909	205	636	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	76.4834	179	636	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	76.4236	154	636	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	76.3649	166	636	95	below_threshold
Paraburkholderia phosphatilytica	strain=7QSK02	GCA_003443895.1	2282883	2282883	type	True	76.3437	175	636	95	below_threshold
Burkholderia paludis	strain=MSh1	GCA_000732615.1	1506587	1506587	type	True	76.3341	232	636	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	76.3284	137	636	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	76.318	167	636	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.3159	138	636	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:05:21,236] [INFO] DFAST Taxonomy check result was written to GCA_025993695.1_ASM2599369v1_genomic.fna/tc_result.tsv
[2023-06-30 19:05:21,236] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:05:21,236] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:05:21,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference/checkm_data
[2023-06-30 19:05:21,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:05:21,269] [INFO] Task started: CheckM
[2023-06-30 19:05:21,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025993695.1_ASM2599369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025993695.1_ASM2599369v1_genomic.fna/checkm_input GCA_025993695.1_ASM2599369v1_genomic.fna/checkm_result
[2023-06-30 19:05:47,196] [INFO] Task succeeded: CheckM
[2023-06-30 19:05:47,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 19:05:47,220] [INFO] ===== Completeness check finished =====
[2023-06-30 19:05:47,221] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:05:47,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025993695.1_ASM2599369v1_genomic.fna/markers.fasta)
[2023-06-30 19:05:47,222] [INFO] Task started: Blastn
[2023-06-30 19:05:47,222] [INFO] Running command: blastn -query GCA_025993695.1_ASM2599369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg628f9293-ae32-48fa-afa0-05f0952b0dbb/dqc_reference/reference_markers_gtdb.fasta -out GCA_025993695.1_ASM2599369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:05:48,548] [INFO] Task succeeded: Blastn
[2023-06-30 19:05:48,553] [INFO] Selected 9 target genomes.
[2023-06-30 19:05:48,554] [INFO] Target genome list was writen to GCA_025993695.1_ASM2599369v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:05:48,556] [INFO] Task started: fastANI
[2023-06-30 19:05:48,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6a26cf-4de8-40e9-8152-717d7e38f690/GCA_025993695.1_ASM2599369v1_genomic.fna.gz --refList GCA_025993695.1_ASM2599369v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025993695.1_ASM2599369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:05:55,328] [INFO] Task succeeded: fastANI
[2023-06-30 19:05:55,341] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:05:55,341] [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_001724855.1	s__SCN-69-89 sp001724855	98.3228	552	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003577305.1	s__SCN-69-89 sp003577305	87.9343	438	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.77	99.54	0.93	0.87	4	-
GCA_001898645.1	s__SCN-69-89 sp001898645	82.3708	435	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCA_003576795.1	s__SCN-69-89 sp003576795	80.7988	310	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724315.1	s__SCN-69-89 sp001724315	80.7607	254	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039575.1	s__SCN-69-89 sp008039575	80.2938	349	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513825.1	s__SCN-69-89 sp012513825	79.3986	296	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307915.1	s__SCN-69-89 sp017307915	79.358	298	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202215.1	s__Quisquiliibacterium transsilvanicum	79.0972	289	636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Quisquiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:05:55,343] [INFO] GTDB search result was written to GCA_025993695.1_ASM2599369v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:05:55,344] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:05:55,349] [INFO] DFAST_QC result json was written to GCA_025993695.1_ASM2599369v1_genomic.fna/dqc_result.json
[2023-06-30 19:05:55,350] [INFO] DFAST_QC completed!
[2023-06-30 19:05:55,350] [INFO] Total running time: 0h1m8s