[2024-01-24 12:06:33,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,214] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference
[2024-01-24 12:06:34,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,384] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg31e38f49-102e-45ba-8a29-ffcb48b39564/GCF_013085255.1_ASM1308525v1_genomic.fna.gz | prodigal -d GCF_013085255.1_ASM1308525v1_genomic.fna/cds.fna -a GCF_013085255.1_ASM1308525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:43,337] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:43,338] [INFO] Task started: HMMsearch
[2024-01-24 12:06:43,338] [INFO] Running command: hmmsearch --tblout GCF_013085255.1_ASM1308525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference/reference_markers.hmm GCF_013085255.1_ASM1308525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:43,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:43,581] [INFO] Found 6/6 markers.
[2024-01-24 12:06:43,720] [INFO] Query marker FASTA was written to GCF_013085255.1_ASM1308525v1_genomic.fna/markers.fasta
[2024-01-24 12:06:43,720] [INFO] Task started: Blastn
[2024-01-24 12:06:43,721] [INFO] Running command: blastn -query GCF_013085255.1_ASM1308525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference/reference_markers.fasta -out GCF_013085255.1_ASM1308525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:44,582] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:44,586] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:44,586] [INFO] Target genome list was writen to GCF_013085255.1_ASM1308525v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:44,593] [INFO] Task started: fastANI
[2024-01-24 12:06:44,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg31e38f49-102e-45ba-8a29-ffcb48b39564/GCF_013085255.1_ASM1308525v1_genomic.fna.gz --refList GCF_013085255.1_ASM1308525v1_genomic.fna/target_genomes.txt --output GCF_013085255.1_ASM1308525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:55,119] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:55,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:55,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:55,138] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:55,138] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:55,138] [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
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	100.0	1069	1070	95	conclusive
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	79.6329	506	1070	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	77.639	248	1070	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	77.587	151	1070	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	77.5548	253	1070	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.2898	126	1070	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.2856	131	1070	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	77.1388	135	1070	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.5493	82	1070	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	76.3679	74	1070	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.2719	71	1070	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.2705	85	1070	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	76.26	96	1070	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.2113	67	1070	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.1608	88	1070	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.1434	88	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:55,140] [INFO] DFAST Taxonomy check result was written to GCF_013085255.1_ASM1308525v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:55,140] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:55,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:55,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference/checkm_data
[2024-01-24 12:06:55,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:55,173] [INFO] Task started: CheckM
[2024-01-24 12:06:55,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013085255.1_ASM1308525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013085255.1_ASM1308525v1_genomic.fna/checkm_input GCF_013085255.1_ASM1308525v1_genomic.fna/checkm_result
[2024-01-24 12:07:25,608] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:25,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:25,631] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:25,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:25,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013085255.1_ASM1308525v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:25,632] [INFO] Task started: Blastn
[2024-01-24 12:07:25,632] [INFO] Running command: blastn -query GCF_013085255.1_ASM1308525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a3ab8e5-58a8-44e0-b5fb-1d6aa668fb5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013085255.1_ASM1308525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:27,267] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:27,271] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:27,271] [INFO] Target genome list was writen to GCF_013085255.1_ASM1308525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:27,282] [INFO] Task started: fastANI
[2024-01-24 12:07:27,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg31e38f49-102e-45ba-8a29-ffcb48b39564/GCF_013085255.1_ASM1308525v1_genomic.fna.gz --refList GCF_013085255.1_ASM1308525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013085255.1_ASM1308525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:36,347] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:36,362] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:36,362] [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
GCF_013085255.1	s__Parvularcula mediterranea	100.0	1070	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014651915.1	s__Parvularcula lutaonensis	79.6536	504	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215175.1	s__Parvularcula sp013215175	77.7586	234	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	77.639	248	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399445.1	s__Parvularcula sp003399445	77.587	151	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	77.5548	253	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	77.3199	137	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640095.1	s__Aquisalinus flavus	77.2856	131	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016742175.1	s__Aliihoeflea sp016742175	76.6008	79	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	76.4725	77	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	76.3012	88	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117415.1	s__Ga0077555 sp900117415	76.2706	72	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	97.09	97.07	0.95	0.91	3	-
GCF_014196455.1	s__Kaistia hirudinis	76.2705	85	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCA_013911975.1	s__Aquabacter sp013911975	75.4176	70	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,364] [INFO] GTDB search result was written to GCF_013085255.1_ASM1308525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:36,365] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:36,369] [INFO] DFAST_QC result json was written to GCF_013085255.1_ASM1308525v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:36,370] [INFO] DFAST_QC completed!
[2024-01-24 12:07:36,370] [INFO] Total running time: 0h1m3s