[2023-06-30 03:48:29,580] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:48:29,582] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:48:29,582] [INFO] DQC Reference Directory: /var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference
[2023-06-30 03:48:30,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:48:30,758] [INFO] Task started: Prodigal
[2023-06-30 03:48:30,758] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc264c09-ce70-4432-9113-576a3bca019b/GCA_016214925.1_ASM1621492v1_genomic.fna.gz | prodigal -d GCA_016214925.1_ASM1621492v1_genomic.fna/cds.fna -a GCA_016214925.1_ASM1621492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:48:37,790] [INFO] Task succeeded: Prodigal
[2023-06-30 03:48:37,790] [INFO] Task started: HMMsearch
[2023-06-30 03:48:37,791] [INFO] Running command: hmmsearch --tblout GCA_016214925.1_ASM1621492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference/reference_markers.hmm GCA_016214925.1_ASM1621492v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:48:38,009] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:48:38,010] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcc264c09-ce70-4432-9113-576a3bca019b/GCA_016214925.1_ASM1621492v1_genomic.fna.gz]
[2023-06-30 03:48:38,034] [INFO] Query marker FASTA was written to GCA_016214925.1_ASM1621492v1_genomic.fna/markers.fasta
[2023-06-30 03:48:38,035] [INFO] Task started: Blastn
[2023-06-30 03:48:38,035] [INFO] Running command: blastn -query GCA_016214925.1_ASM1621492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference/reference_markers.fasta -out GCA_016214925.1_ASM1621492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:48:38,857] [INFO] Task succeeded: Blastn
[2023-06-30 03:48:38,861] [INFO] Selected 27 target genomes.
[2023-06-30 03:48:38,861] [INFO] Target genome list was writen to GCA_016214925.1_ASM1621492v1_genomic.fna/target_genomes.txt
[2023-06-30 03:48:38,863] [INFO] Task started: fastANI
[2023-06-30 03:48:38,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc264c09-ce70-4432-9113-576a3bca019b/GCA_016214925.1_ASM1621492v1_genomic.fna.gz --refList GCA_016214925.1_ASM1621492v1_genomic.fna/target_genomes.txt --output GCA_016214925.1_ASM1621492v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:48:54,732] [INFO] Task succeeded: fastANI
[2023-06-30 03:48:54,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:48:54,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:48:54,756] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:48:54,756] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:48:54,756] [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
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.65	200	719	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.4042	112	719	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.9454	160	719	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.804	114	719	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.7943	77	719	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.7473	98	719	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.7195	87	719	95	below_threshold
Methylogaea oryzae	strain=JCM 16910	GCA_001312345.1	1295382	1295382	type	True	76.6707	54	719	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.5343	106	719	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.399	76	719	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3585	143	719	95	below_threshold
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	76.3288	55	719	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.2947	83	719	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.2907	68	719	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	76.2489	61	719	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	76.163	89	719	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.136	66	719	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.113	67	719	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.0337	80	719	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.9966	80	719	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.991	79	719	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	75.5499	65	719	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:48:54,758] [INFO] DFAST Taxonomy check result was written to GCA_016214925.1_ASM1621492v1_genomic.fna/tc_result.tsv
[2023-06-30 03:48:54,759] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:48:54,759] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:48:54,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference/checkm_data
[2023-06-30 03:48:54,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:48:54,790] [INFO] Task started: CheckM
[2023-06-30 03:48:54,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016214925.1_ASM1621492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016214925.1_ASM1621492v1_genomic.fna/checkm_input GCA_016214925.1_ASM1621492v1_genomic.fna/checkm_result
[2023-06-30 03:49:20,782] [INFO] Task succeeded: CheckM
[2023-06-30 03:49:20,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:49:20,802] [INFO] ===== Completeness check finished =====
[2023-06-30 03:49:20,803] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:49:20,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016214925.1_ASM1621492v1_genomic.fna/markers.fasta)
[2023-06-30 03:49:20,803] [INFO] Task started: Blastn
[2023-06-30 03:49:20,804] [INFO] Running command: blastn -query GCA_016214925.1_ASM1621492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga279483c-9034-43b5-b9a3-0b9584c47682/dqc_reference/reference_markers_gtdb.fasta -out GCA_016214925.1_ASM1621492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:49:22,268] [INFO] Task succeeded: Blastn
[2023-06-30 03:49:22,273] [INFO] Selected 20 target genomes.
[2023-06-30 03:49:22,273] [INFO] Target genome list was writen to GCA_016214925.1_ASM1621492v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:49:22,281] [INFO] Task started: fastANI
[2023-06-30 03:49:22,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc264c09-ce70-4432-9113-576a3bca019b/GCA_016214925.1_ASM1621492v1_genomic.fna.gz --refList GCA_016214925.1_ASM1621492v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016214925.1_ASM1621492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:49:34,527] [INFO] Task succeeded: fastANI
[2023-06-30 03:49:34,544] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:49:34,545] [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_016214925.1	s__JAHJQQ01 sp016214925	99.9999	696	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016218375.1	s__JAHJQQ01 sp016218375	86.3216	516	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819175.1	s__JAHJQQ01 sp018819175	79.0147	340	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	77.6655	199	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.6378	210	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_002699185.1	s__Thiohalobacter sp002699185	77.5014	169	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.3542	144	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	77.0072	75	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.9457	177	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.9164	162	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801995.1	s__YD12-FULL-61-37 sp001801995	76.7879	50	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__YD12-FULL-61-37	95.0	99.93	99.93	0.98	0.98	2	-
GCF_000754095.2	s__Acidihalobacter prosperus	76.696	88	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.5875	125	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_018813765.1	s__Sideroxydans sp018813765	76.381	70	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_003989065.1	s__RXIW01 sp003989065	76.3735	71	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	76.2475	70	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003989075.1	s__RXIX01 sp003989075	76.0177	75	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:49:34,547] [INFO] GTDB search result was written to GCA_016214925.1_ASM1621492v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:49:34,547] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:49:34,552] [INFO] DFAST_QC result json was written to GCA_016214925.1_ASM1621492v1_genomic.fna/dqc_result.json
[2023-06-30 03:49:34,552] [INFO] DFAST_QC completed!
[2023-06-30 03:49:34,552] [INFO] Total running time: 0h1m5s