[2023-06-18 22:56:45,420] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:56:45,425] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:56:45,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference
[2023-06-18 22:56:46,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:56:46,761] [INFO] Task started: Prodigal
[2023-06-18 22:56:46,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e50e2ac-116c-4ce8-9f73-98f49ae88eb0/GCA_018240665.1_ASM1824066v1_genomic.fna.gz | prodigal -d GCA_018240665.1_ASM1824066v1_genomic.fna/cds.fna -a GCA_018240665.1_ASM1824066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:56:57,448] [INFO] Task succeeded: Prodigal
[2023-06-18 22:56:57,449] [INFO] Task started: HMMsearch
[2023-06-18 22:56:57,449] [INFO] Running command: hmmsearch --tblout GCA_018240665.1_ASM1824066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference/reference_markers.hmm GCA_018240665.1_ASM1824066v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:56:57,748] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:56:57,749] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e50e2ac-116c-4ce8-9f73-98f49ae88eb0/GCA_018240665.1_ASM1824066v1_genomic.fna.gz]
[2023-06-18 22:56:57,792] [INFO] Query marker FASTA was written to GCA_018240665.1_ASM1824066v1_genomic.fna/markers.fasta
[2023-06-18 22:56:57,793] [INFO] Task started: Blastn
[2023-06-18 22:56:57,793] [INFO] Running command: blastn -query GCA_018240665.1_ASM1824066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference/reference_markers.fasta -out GCA_018240665.1_ASM1824066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:56:58,698] [INFO] Task succeeded: Blastn
[2023-06-18 22:56:58,702] [INFO] Selected 14 target genomes.
[2023-06-18 22:56:58,703] [INFO] Target genome list was writen to GCA_018240665.1_ASM1824066v1_genomic.fna/target_genomes.txt
[2023-06-18 22:56:58,705] [INFO] Task started: fastANI
[2023-06-18 22:56:58,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e50e2ac-116c-4ce8-9f73-98f49ae88eb0/GCA_018240665.1_ASM1824066v1_genomic.fna.gz --refList GCA_018240665.1_ASM1824066v1_genomic.fna/target_genomes.txt --output GCA_018240665.1_ASM1824066v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:14,152] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:14,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:14,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:14,173] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:14,173] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:57:14,173] [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
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	83.0681	822	1085	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	82.9809	800	1085	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	82.121	733	1085	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	79.1285	574	1085	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	77.3025	345	1085	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.2833	346	1085	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.1195	363	1085	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.998	305	1085	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.9578	265	1085	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.9023	238	1085	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.8509	231	1085	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.7932	169	1085	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.3338	160	1085	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.3218	161	1085	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:57:14,175] [INFO] DFAST Taxonomy check result was written to GCA_018240665.1_ASM1824066v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:14,176] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:14,176] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:14,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference/checkm_data
[2023-06-18 22:57:14,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:14,224] [INFO] Task started: CheckM
[2023-06-18 22:57:14,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018240665.1_ASM1824066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018240665.1_ASM1824066v1_genomic.fna/checkm_input GCA_018240665.1_ASM1824066v1_genomic.fna/checkm_result
[2023-06-18 22:57:48,727] [INFO] Task succeeded: CheckM
[2023-06-18 22:57:48,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:57:48,758] [INFO] ===== Completeness check finished =====
[2023-06-18 22:57:48,758] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:57:48,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018240665.1_ASM1824066v1_genomic.fna/markers.fasta)
[2023-06-18 22:57:48,759] [INFO] Task started: Blastn
[2023-06-18 22:57:48,759] [INFO] Running command: blastn -query GCA_018240665.1_ASM1824066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg679df4e3-61c0-4e0f-a072-d6bc9b939a94/dqc_reference/reference_markers_gtdb.fasta -out GCA_018240665.1_ASM1824066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:50,433] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:50,437] [INFO] Selected 14 target genomes.
[2023-06-18 22:57:50,437] [INFO] Target genome list was writen to GCA_018240665.1_ASM1824066v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:57:50,467] [INFO] Task started: fastANI
[2023-06-18 22:57:50,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e50e2ac-116c-4ce8-9f73-98f49ae88eb0/GCA_018240665.1_ASM1824066v1_genomic.fna.gz --refList GCA_018240665.1_ASM1824066v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018240665.1_ASM1824066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:58:06,751] [INFO] Task succeeded: fastANI
[2023-06-18 22:58:06,766] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:58:06,766] [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_018240695.1	s__Reyranella sp018240695	96.9223	908	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	conclusive
GCA_903832005.1	s__Reyranella aerosaccus_B	85.639	891	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
GCA_903915535.1	s__Reyranella aerosaccus_C	85.4017	851	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.05	99.05	0.90	0.90	2	-
GCA_903839865.1	s__Reyranella aerosaccus_A	85.2316	790	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.29	98.98	0.87	0.83	3	-
GCA_004296815.1	s__Reyranella sp004296815	83.578	614	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	83.2239	610	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039055.1	s__Reyranella sp019039055	83.0755	786	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	83.0255	830	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	82.8993	752	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297265.1	s__Reyranella sp004297265	82.8508	800	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205335.1	s__Reyranella sp013205335	82.2834	625	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897995.1	s__Reyranella sp001897995	82.2545	718	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.19	98.73	0.86	0.86	3	-
GCF_000312425.1	s__Reyranella massiliensis	82.1357	731	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297405.1	s__Reyranella sp004297405	81.9304	731	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:58:06,767] [INFO] GTDB search result was written to GCA_018240665.1_ASM1824066v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:58:06,768] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:58:06,771] [INFO] DFAST_QC result json was written to GCA_018240665.1_ASM1824066v1_genomic.fna/dqc_result.json
[2023-06-18 22:58:06,771] [INFO] DFAST_QC completed!
[2023-06-18 22:58:06,772] [INFO] Total running time: 0h1m21s