[2023-06-19 03:05:41,438] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:05:41,441] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:05:41,441] [INFO] DQC Reference Directory: /var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference
[2023-06-19 03:05:43,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:05:43,747] [INFO] Task started: Prodigal
[2023-06-19 03:05:43,748] [INFO] Running command: gunzip -c /var/lib/cwl/stga4916ba1-6b58-40fa-8690-31e42e15c2ff/GCA_018671795.1_ASM1867179v1_genomic.fna.gz | prodigal -d GCA_018671795.1_ASM1867179v1_genomic.fna/cds.fna -a GCA_018671795.1_ASM1867179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:05:51,719] [INFO] Task succeeded: Prodigal
[2023-06-19 03:05:51,720] [INFO] Task started: HMMsearch
[2023-06-19 03:05:51,720] [INFO] Running command: hmmsearch --tblout GCA_018671795.1_ASM1867179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference/reference_markers.hmm GCA_018671795.1_ASM1867179v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:05:51,959] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:05:51,960] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga4916ba1-6b58-40fa-8690-31e42e15c2ff/GCA_018671795.1_ASM1867179v1_genomic.fna.gz]
[2023-06-19 03:05:51,993] [INFO] Query marker FASTA was written to GCA_018671795.1_ASM1867179v1_genomic.fna/markers.fasta
[2023-06-19 03:05:51,993] [INFO] Task started: Blastn
[2023-06-19 03:05:51,994] [INFO] Running command: blastn -query GCA_018671795.1_ASM1867179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference/reference_markers.fasta -out GCA_018671795.1_ASM1867179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:05:52,609] [INFO] Task succeeded: Blastn
[2023-06-19 03:05:52,615] [INFO] Selected 23 target genomes.
[2023-06-19 03:05:52,615] [INFO] Target genome list was writen to GCA_018671795.1_ASM1867179v1_genomic.fna/target_genomes.txt
[2023-06-19 03:05:52,617] [INFO] Task started: fastANI
[2023-06-19 03:05:52,617] [INFO] Running command: fastANI --query /var/lib/cwl/stga4916ba1-6b58-40fa-8690-31e42e15c2ff/GCA_018671795.1_ASM1867179v1_genomic.fna.gz --refList GCA_018671795.1_ASM1867179v1_genomic.fna/target_genomes.txt --output GCA_018671795.1_ASM1867179v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:06:10,903] [INFO] Task succeeded: fastANI
[2023-06-19 03:06:10,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:06:10,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:06:10,922] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:06:10,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:06:10,922] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.9398	84	701	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.9199	87	701	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	75.892	58	701	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.7239	66	701	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	75.7008	57	701	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	75.7008	57	701	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.6776	78	701	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.6734	88	701	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	75.6274	64	701	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.5821	67	701	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.5813	53	701	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.5471	69	701	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.5128	55	701	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.4812	71	701	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.4305	66	701	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.4247	82	701	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.3727	76	701	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	75.2727	52	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:06:10,925] [INFO] DFAST Taxonomy check result was written to GCA_018671795.1_ASM1867179v1_genomic.fna/tc_result.tsv
[2023-06-19 03:06:10,925] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:06:10,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:06:10,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference/checkm_data
[2023-06-19 03:06:10,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:06:10,956] [INFO] Task started: CheckM
[2023-06-19 03:06:10,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018671795.1_ASM1867179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018671795.1_ASM1867179v1_genomic.fna/checkm_input GCA_018671795.1_ASM1867179v1_genomic.fna/checkm_result
[2023-06-19 03:06:36,576] [INFO] Task succeeded: CheckM
[2023-06-19 03:06:36,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:06:36,601] [INFO] ===== Completeness check finished =====
[2023-06-19 03:06:36,601] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:06:36,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018671795.1_ASM1867179v1_genomic.fna/markers.fasta)
[2023-06-19 03:06:36,602] [INFO] Task started: Blastn
[2023-06-19 03:06:36,602] [INFO] Running command: blastn -query GCA_018671795.1_ASM1867179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6297356-55b5-42f9-ac91-82d86d077d84/dqc_reference/reference_markers_gtdb.fasta -out GCA_018671795.1_ASM1867179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:06:37,475] [INFO] Task succeeded: Blastn
[2023-06-19 03:06:37,479] [INFO] Selected 11 target genomes.
[2023-06-19 03:06:37,480] [INFO] Target genome list was writen to GCA_018671795.1_ASM1867179v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:06:37,482] [INFO] Task started: fastANI
[2023-06-19 03:06:37,482] [INFO] Running command: fastANI --query /var/lib/cwl/stga4916ba1-6b58-40fa-8690-31e42e15c2ff/GCA_018671795.1_ASM1867179v1_genomic.fna.gz --refList GCA_018671795.1_ASM1867179v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018671795.1_ASM1867179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:06:44,756] [INFO] Task succeeded: fastANI
[2023-06-19 03:06:44,773] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:06:44,774] [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_018702955.1	s__UBA8079 sp018702955	99.6066	666	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	conclusive
GCA_018667335.1	s__UBA8079 sp018667335	84.8791	621	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_002727315.1	s__UBA8079 sp002727315	78.9218	310	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	78.7354	353	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.0753	282	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	77.1226	204	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003285.1	s__JABDJY01 sp013003285	76.8537	152	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	76.6121	186	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCF_003173715.1	s__Methylobacterium durans	75.2727	52	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:06:44,776] [INFO] GTDB search result was written to GCA_018671795.1_ASM1867179v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:06:44,777] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:06:44,783] [INFO] DFAST_QC result json was written to GCA_018671795.1_ASM1867179v1_genomic.fna/dqc_result.json
[2023-06-19 03:06:44,784] [INFO] DFAST_QC completed!
[2023-06-19 03:06:44,784] [INFO] Total running time: 0h1m3s