[2024-01-24 13:45:46,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference
[2024-01-24 13:45:48,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:48,169] [INFO] Task started: Prodigal
[2024-01-24 13:45:48,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg67037992-0739-4f09-870d-2ab006e29dda/GCF_007556775.1_ASM755677v1_genomic.fna.gz | prodigal -d GCF_007556775.1_ASM755677v1_genomic.fna/cds.fna -a GCF_007556775.1_ASM755677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:56,598] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:56,599] [INFO] Task started: HMMsearch
[2024-01-24 13:45:56,599] [INFO] Running command: hmmsearch --tblout GCF_007556775.1_ASM755677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference/reference_markers.hmm GCF_007556775.1_ASM755677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:56,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:56,917] [INFO] Found 6/6 markers.
[2024-01-24 13:45:56,954] [INFO] Query marker FASTA was written to GCF_007556775.1_ASM755677v1_genomic.fna/markers.fasta
[2024-01-24 13:45:56,954] [INFO] Task started: Blastn
[2024-01-24 13:45:56,955] [INFO] Running command: blastn -query GCF_007556775.1_ASM755677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference/reference_markers.fasta -out GCF_007556775.1_ASM755677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:58,016] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:58,019] [INFO] Selected 24 target genomes.
[2024-01-24 13:45:58,020] [INFO] Target genome list was writen to GCF_007556775.1_ASM755677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:58,064] [INFO] Task started: fastANI
[2024-01-24 13:45:58,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg67037992-0739-4f09-870d-2ab006e29dda/GCF_007556775.1_ASM755677v1_genomic.fna.gz --refList GCF_007556775.1_ASM755677v1_genomic.fna/target_genomes.txt --output GCF_007556775.1_ASM755677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:15,955] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:15,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:15,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:15,976] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:15,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:15,977] [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
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	83.1024	605	865	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.2347	567	865	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	82.0809	552	865	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	82.0476	528	865	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.9406	498	865	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.8282	515	865	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	81.7164	508	865	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.6352	582	865	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.5838	543	865	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.398	549	865	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.2997	516	865	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.2324	542	865	95	below_threshold
Lysobacter oculi	strain=83-4	GCA_003293695.1	2698682	2698682	type	True	81.1883	493	865	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.1333	568	865	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.0974	496	865	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.0724	552	865	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	80.9836	544	865	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	80.8779	508	865	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	80.8504	520	865	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	80.8287	477	865	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	80.7	485	865	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.6117	511	865	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	80.2982	491	865	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	79.7145	425	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:15,979] [INFO] DFAST Taxonomy check result was written to GCF_007556775.1_ASM755677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:15,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:15,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:15,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference/checkm_data
[2024-01-24 13:46:15,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:16,010] [INFO] Task started: CheckM
[2024-01-24 13:46:16,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007556775.1_ASM755677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007556775.1_ASM755677v1_genomic.fna/checkm_input GCF_007556775.1_ASM755677v1_genomic.fna/checkm_result
[2024-01-24 13:46:48,841] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:48,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:48,869] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:48,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:48,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007556775.1_ASM755677v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:48,871] [INFO] Task started: Blastn
[2024-01-24 13:46:48,871] [INFO] Running command: blastn -query GCF_007556775.1_ASM755677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde1efb29-7d4e-4759-8e59-773049195e4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007556775.1_ASM755677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:51,062] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:51,066] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:51,066] [INFO] Target genome list was writen to GCF_007556775.1_ASM755677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:51,110] [INFO] Task started: fastANI
[2024-01-24 13:46:51,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg67037992-0739-4f09-870d-2ab006e29dda/GCF_007556775.1_ASM755677v1_genomic.fna.gz --refList GCF_007556775.1_ASM755677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007556775.1_ASM755677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:05,657] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:05,680] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:05,680] [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_007556775.1	s__Thermomonas lycopersici	100.0	865	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006337105.1	s__Thermomonas sp006337105	83.0957	605	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	82.5769	526	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_014395425.1	s__Thermomonas brevis	82.4826	559	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	82.2497	462	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	82.214	568	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416885.1	s__Luteimonas_B sp003416885	82.1102	549	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	82.0641	437	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	82.0271	530	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	81.9171	357	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	81.8372	514	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305095.1	s__Thermomonas sp017305095	81.5904	492	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	81.586	507	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	81.2353	541	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	81.2114	599	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_018406645.1	s__Lysobacter_A helvus	81.2092	523	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017308985.1	s__Lysobacter sp017308985	81.2052	561	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016774335.1	s__Luteimonas sp016774335	81.0806	551	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382285.1	s__Lysobacter soli	80.9956	543	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	80.5516	506	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655355.1	s__Pseudoxanthomonas_A sp015655355	80.2447	378	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:05,682] [INFO] GTDB search result was written to GCF_007556775.1_ASM755677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:05,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:05,687] [INFO] DFAST_QC result json was written to GCF_007556775.1_ASM755677v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:05,687] [INFO] DFAST_QC completed!
[2024-01-24 13:47:05,687] [INFO] Total running time: 0h1m19s