[2024-01-25 19:02:20,595] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,597] [INFO] DQC Reference Directory: /var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference
[2024-01-25 19:02:21,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,770] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg28a1deb9-eb93-4d89-bfdd-1a57af5288cc/GCF_002895945.1_ASM289594v1_genomic.fna.gz | prodigal -d GCF_002895945.1_ASM289594v1_genomic.fna/cds.fna -a GCF_002895945.1_ASM289594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:30,829] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:30,829] [INFO] Task started: HMMsearch
[2024-01-25 19:02:30,830] [INFO] Running command: hmmsearch --tblout GCF_002895945.1_ASM289594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference/reference_markers.hmm GCF_002895945.1_ASM289594v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:31,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:31,031] [INFO] Found 6/6 markers.
[2024-01-25 19:02:31,054] [INFO] Query marker FASTA was written to GCF_002895945.1_ASM289594v1_genomic.fna/markers.fasta
[2024-01-25 19:02:31,055] [INFO] Task started: Blastn
[2024-01-25 19:02:31,055] [INFO] Running command: blastn -query GCF_002895945.1_ASM289594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference/reference_markers.fasta -out GCF_002895945.1_ASM289594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:31,938] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:31,941] [INFO] Selected 23 target genomes.
[2024-01-25 19:02:31,941] [INFO] Target genome list was writen to GCF_002895945.1_ASM289594v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:31,966] [INFO] Task started: fastANI
[2024-01-25 19:02:31,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a1deb9-eb93-4d89-bfdd-1a57af5288cc/GCF_002895945.1_ASM289594v1_genomic.fna.gz --refList GCF_002895945.1_ASM289594v1_genomic.fna/target_genomes.txt --output GCF_002895945.1_ASM289594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:47,386] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:47,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:47,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:47,400] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:47,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:47,401] [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
Lysobacter silvestris	strain=AM20-91	GCA_002895945.1	1645665	1645665	type	True	100.0	945	947	95	conclusive
Lysobacter oculi	strain=83-4	GCA_003293695.1	2698682	2698682	type	True	80.8308	467	947	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.7173	475	947	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	80.0711	460	947	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	80.0165	379	947	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	79.9222	389	947	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	79.906	460	947	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.7921	461	947	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	79.7579	449	947	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	79.5588	443	947	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	79.5053	372	947	95	below_threshold
Lysobacter tolerans	strain=UM1	GCA_900155935.1	1604334	1604334	type	True	79.4953	334	947	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.4927	378	947	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	79.409	434	947	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.3097	426	947	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	79.3076	408	947	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.2814	437	947	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	79.1812	429	947	95	below_threshold
Luteimonas fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	79.1719	394	947	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	79.1171	396	947	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	79.0069	392	947	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	78.9953	393	947	95	below_threshold
Stenotrophomonas chelatiphaga	strain=DSM 21508	GCA_001431535.1	517011	517011	type	True	78.6164	340	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:47,402] [INFO] DFAST Taxonomy check result was written to GCF_002895945.1_ASM289594v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:47,403] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:47,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:47,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference/checkm_data
[2024-01-25 19:02:47,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:47,434] [INFO] Task started: CheckM
[2024-01-25 19:02:47,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002895945.1_ASM289594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002895945.1_ASM289594v1_genomic.fna/checkm_input GCF_002895945.1_ASM289594v1_genomic.fna/checkm_result
[2024-01-25 19:03:35,195] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:35,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:35,216] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:35,216] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:35,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002895945.1_ASM289594v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:35,217] [INFO] Task started: Blastn
[2024-01-25 19:03:35,217] [INFO] Running command: blastn -query GCF_002895945.1_ASM289594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefedcc7c-ac2e-4462-acd5-f6bcd94e55d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002895945.1_ASM289594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:36,966] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:36,969] [INFO] Selected 10 target genomes.
[2024-01-25 19:03:36,970] [INFO] Target genome list was writen to GCF_002895945.1_ASM289594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:36,978] [INFO] Task started: fastANI
[2024-01-25 19:03:36,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a1deb9-eb93-4d89-bfdd-1a57af5288cc/GCF_002895945.1_ASM289594v1_genomic.fna.gz --refList GCF_002895945.1_ASM289594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002895945.1_ASM289594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:43,987] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:43,994] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:43,994] [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_002895945.1	s__Lysobacter_B silvestris	100.0	945	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018242425.1	s__Lysobacter_B sp018242425	86.3461	691	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	98.53	98.53	0.95	0.95	2	-
GCA_018242405.1	s__Lysobacter_B sp018242405	86.0471	579	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242465.1	s__Lysobacter_B sp018242465	84.9962	612	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293695.1	s__Lysobacter_B oculi	80.8397	466	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	80.7241	474	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	80.3642	467	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556775.1	s__Thermomonas lycopersici	80.3099	437	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357985.1	s__Luteimonas aestuarii	79.3075	408	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	79.0511	442	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:43,996] [INFO] GTDB search result was written to GCF_002895945.1_ASM289594v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:43,996] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:44,000] [INFO] DFAST_QC result json was written to GCF_002895945.1_ASM289594v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:44,000] [INFO] DFAST_QC completed!
[2024-01-25 19:03:44,000] [INFO] Total running time: 0h1m23s