[2023-06-17 12:25:01,627] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:25:01,629] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:25:01,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference
[2023-06-17 12:25:02,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:25:02,926] [INFO] Task started: Prodigal
[2023-06-17 12:25:02,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e16b1f5-b584-4beb-9754-80bacf428046/GCA_009993005.1_ASM999300v1_genomic.fna.gz | prodigal -d GCA_009993005.1_ASM999300v1_genomic.fna/cds.fna -a GCA_009993005.1_ASM999300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:25:13,024] [INFO] Task succeeded: Prodigal
[2023-06-17 12:25:13,025] [INFO] Task started: HMMsearch
[2023-06-17 12:25:13,025] [INFO] Running command: hmmsearch --tblout GCA_009993005.1_ASM999300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference/reference_markers.hmm GCA_009993005.1_ASM999300v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:25:13,276] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:25:13,278] [INFO] Found 6/6 markers.
[2023-06-17 12:25:13,329] [INFO] Query marker FASTA was written to GCA_009993005.1_ASM999300v1_genomic.fna/markers.fasta
[2023-06-17 12:25:13,330] [INFO] Task started: Blastn
[2023-06-17 12:25:13,330] [INFO] Running command: blastn -query GCA_009993005.1_ASM999300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference/reference_markers.fasta -out GCA_009993005.1_ASM999300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:14,299] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:14,304] [INFO] Selected 23 target genomes.
[2023-06-17 12:25:14,305] [INFO] Target genome list was writen to GCA_009993005.1_ASM999300v1_genomic.fna/target_genomes.txt
[2023-06-17 12:25:14,311] [INFO] Task started: fastANI
[2023-06-17 12:25:14,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e16b1f5-b584-4beb-9754-80bacf428046/GCA_009993005.1_ASM999300v1_genomic.fna.gz --refList GCA_009993005.1_ASM999300v1_genomic.fna/target_genomes.txt --output GCA_009993005.1_ASM999300v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:25:31,983] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:31,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:25:31,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:25:32,013] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:25:32,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:25:32,014] [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
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	79.3427	499	1047	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.2977	510	1047	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.1135	511	1047	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.8788	458	1047	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	78.8771	450	1047	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.8703	466	1047	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	78.8589	466	1047	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8336	450	1047	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.8146	476	1047	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.7527	463	1047	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.5499	458	1047	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	78.507	473	1047	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	78.3844	410	1047	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.3777	459	1047	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.3699	457	1047	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.2195	390	1047	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	78.1078	410	1047	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.0642	488	1047	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	78.0493	417	1047	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	77.995	394	1047	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.7868	344	1047	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.2945	347	1047	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.845	246	1047	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:25:32,016] [INFO] DFAST Taxonomy check result was written to GCA_009993005.1_ASM999300v1_genomic.fna/tc_result.tsv
[2023-06-17 12:25:32,016] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:25:32,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:32,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference/checkm_data
[2023-06-17 12:25:32,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:32,053] [INFO] Task started: CheckM
[2023-06-17 12:25:32,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009993005.1_ASM999300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009993005.1_ASM999300v1_genomic.fna/checkm_input GCA_009993005.1_ASM999300v1_genomic.fna/checkm_result
[2023-06-17 12:26:09,598] [INFO] Task succeeded: CheckM
[2023-06-17 12:26:09,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 12:26:09,627] [INFO] ===== Completeness check finished =====
[2023-06-17 12:26:09,627] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:26:09,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009993005.1_ASM999300v1_genomic.fna/markers.fasta)
[2023-06-17 12:26:09,628] [INFO] Task started: Blastn
[2023-06-17 12:26:09,628] [INFO] Running command: blastn -query GCA_009993005.1_ASM999300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57dddf5d-691d-4dea-8a7b-89ebdd6c5001/dqc_reference/reference_markers_gtdb.fasta -out GCA_009993005.1_ASM999300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:26:11,403] [INFO] Task succeeded: Blastn
[2023-06-17 12:26:11,409] [INFO] Selected 21 target genomes.
[2023-06-17 12:26:11,409] [INFO] Target genome list was writen to GCA_009993005.1_ASM999300v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:26:11,431] [INFO] Task started: fastANI
[2023-06-17 12:26:11,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e16b1f5-b584-4beb-9754-80bacf428046/GCA_009993005.1_ASM999300v1_genomic.fna.gz --refList GCA_009993005.1_ASM999300v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009993005.1_ASM999300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:26:25,444] [INFO] Task succeeded: fastANI
[2023-06-17 12:26:25,467] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:26:25,467] [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_009993005.1	s__JAACUH01 sp009993005	100.0	1038	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	conclusive
GCA_016125575.1	s__JAACUH01 sp016125575	79.5043	544	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	79.3121	503	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	79.2792	495	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.1048	512	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359765.1	s__Roseovarius sp014359765	78.9646	402	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.9405	339	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.8884	457	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	78.8772	464	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000466965.1	s__Limimaricola cinnabarinus	78.8672	451	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	78.7668	461	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	78.6557	346	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	78.5144	415	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.4648	434	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	78.4398	306	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	78.219	439	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	78.1414	343	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002925845.1	s__Roseovarius nitratireducens	78.0823	414	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_004000435.1	s__Flavimaricola sp004000435	78.0646	488	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_017872975.1	s__Rubellimicrobium aerolatum	77.961	398	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117005.1	s__Pararhodobacter sp007117005	77.9022	303	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.98	98.98	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-17 12:26:25,470] [INFO] GTDB search result was written to GCA_009993005.1_ASM999300v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:26:25,470] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:26:25,475] [INFO] DFAST_QC result json was written to GCA_009993005.1_ASM999300v1_genomic.fna/dqc_result.json
[2023-06-17 12:26:25,475] [INFO] DFAST_QC completed!
[2023-06-17 12:26:25,476] [INFO] Total running time: 0h1m24s