[2024-01-24 12:39:33,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:33,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:33,253] [INFO] DQC Reference Directory: /var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference
[2024-01-24 12:39:34,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:34,454] [INFO] Task started: Prodigal
[2024-01-24 12:39:34,455] [INFO] Running command: gunzip -c /var/lib/cwl/stga9efe1ef-e7c9-4df3-8f54-c0fb1e6872d1/GCF_011300455.1_ASM1130045v1_genomic.fna.gz | prodigal -d GCF_011300455.1_ASM1130045v1_genomic.fna/cds.fna -a GCF_011300455.1_ASM1130045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:42,593] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:42,593] [INFO] Task started: HMMsearch
[2024-01-24 12:39:42,593] [INFO] Running command: hmmsearch --tblout GCF_011300455.1_ASM1130045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference/reference_markers.hmm GCF_011300455.1_ASM1130045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:42,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:42,859] [INFO] Found 6/6 markers.
[2024-01-24 12:39:42,887] [INFO] Query marker FASTA was written to GCF_011300455.1_ASM1130045v1_genomic.fna/markers.fasta
[2024-01-24 12:39:42,888] [INFO] Task started: Blastn
[2024-01-24 12:39:42,888] [INFO] Running command: blastn -query GCF_011300455.1_ASM1130045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference/reference_markers.fasta -out GCF_011300455.1_ASM1130045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:43,730] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:43,734] [INFO] Selected 17 target genomes.
[2024-01-24 12:39:43,735] [INFO] Target genome list was writen to GCF_011300455.1_ASM1130045v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:43,743] [INFO] Task started: fastANI
[2024-01-24 12:39:43,743] [INFO] Running command: fastANI --query /var/lib/cwl/stga9efe1ef-e7c9-4df3-8f54-c0fb1e6872d1/GCF_011300455.1_ASM1130045v1_genomic.fna.gz --refList GCF_011300455.1_ASM1130045v1_genomic.fna/target_genomes.txt --output GCF_011300455.1_ASM1130045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:52,845] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:52,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:52,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:52,860] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:39:52,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:52,860] [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
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	100.0	906	906	95	conclusive
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.1995	317	906	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.1689	344	906	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.0832	301	906	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.081	307	906	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	79.0673	318	906	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	79.0516	311	906	95	below_threshold
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	78.9903	328	906	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	78.9901	290	906	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	78.88	303	906	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.8612	284	906	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.7978	274	906	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.7541	208	906	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	77.6128	192	906	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	77.6068	189	906	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.6032	211	906	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	75.8956	52	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:52,863] [INFO] DFAST Taxonomy check result was written to GCF_011300455.1_ASM1130045v1_genomic.fna/tc_result.tsv
[2024-01-24 12:39:52,864] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:52,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:52,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference/checkm_data
[2024-01-24 12:39:52,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:52,898] [INFO] Task started: CheckM
[2024-01-24 12:39:52,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011300455.1_ASM1130045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011300455.1_ASM1130045v1_genomic.fna/checkm_input GCF_011300455.1_ASM1130045v1_genomic.fna/checkm_result
[2024-01-24 12:40:21,809] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:21,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:21,833] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:21,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:21,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011300455.1_ASM1130045v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:21,834] [INFO] Task started: Blastn
[2024-01-24 12:40:21,834] [INFO] Running command: blastn -query GCF_011300455.1_ASM1130045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb233ea25-4453-4757-8e15-c8fa6bee0b74/dqc_reference/reference_markers_gtdb.fasta -out GCF_011300455.1_ASM1130045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:23,284] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:23,289] [INFO] Selected 23 target genomes.
[2024-01-24 12:40:23,289] [INFO] Target genome list was writen to GCF_011300455.1_ASM1130045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:23,305] [INFO] Task started: fastANI
[2024-01-24 12:40:23,306] [INFO] Running command: fastANI --query /var/lib/cwl/stga9efe1ef-e7c9-4df3-8f54-c0fb1e6872d1/GCF_011300455.1_ASM1130045v1_genomic.fna.gz --refList GCF_011300455.1_ASM1130045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011300455.1_ASM1130045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:36,649] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:36,668] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:36,668] [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_011300455.1	s__Sphingomicrobium piscis	100.0	906	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	79.2145	316	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	79.1689	344	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	79.0989	300	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302055.1	s__Sphingomicrobium sinipercae	79.082	317	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396785.1	s__Sphingomicrobium lutea	79.0663	310	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924655.1	s__Sphingomicrobium sp016924655	78.9901	290	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873475.1	s__Sphingomicrobium sp014873475	78.9452	325	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	78.9418	281	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.9082	300	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	78.8254	287	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	78.7978	274	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620665.1	s__Sphingomicrobium sp000620665	78.7676	315	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	78.5765	281	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806265.1	s__Sphingomicrobium sp902806265	78.5412	276	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	78.5224	328	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812805.1	s__Sphingomicrobium sp013812805	78.4193	220	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591045.1	s__Sphingopyxis granuli	77.9065	182	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	77.7562	208	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563265.1	s__Sphingobium sp001563265	77.4653	188	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.38	97.84	0.74	0.68	3	-
GCF_001556185.1	s__Sphingomonas sp001556185	77.4388	173	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.51	96.51	0.87	0.87	2	-
GCF_014207235.1	s__Sphingopyxis sp014207235	77.3426	185	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562255.1	s__Bosea sp001562255	76.331	84	906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:36,670] [INFO] GTDB search result was written to GCF_011300455.1_ASM1130045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:36,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:36,674] [INFO] DFAST_QC result json was written to GCF_011300455.1_ASM1130045v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:36,675] [INFO] DFAST_QC completed!
[2024-01-24 12:40:36,675] [INFO] Total running time: 0h1m3s