[2024-01-24 11:05:49,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference
[2024-01-24 11:05:51,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,281] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,281] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6d4b350-8c62-44c9-ab7b-8e7297387d4e/GCF_022808325.1_ASM2280832v1_genomic.fna.gz | prodigal -d GCF_022808325.1_ASM2280832v1_genomic.fna/cds.fna -a GCF_022808325.1_ASM2280832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:59,597] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:59,597] [INFO] Task started: HMMsearch
[2024-01-24 11:05:59,597] [INFO] Running command: hmmsearch --tblout GCF_022808325.1_ASM2280832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference/reference_markers.hmm GCF_022808325.1_ASM2280832v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:59,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:59,786] [INFO] Found 6/6 markers.
[2024-01-24 11:05:59,812] [INFO] Query marker FASTA was written to GCF_022808325.1_ASM2280832v1_genomic.fna/markers.fasta
[2024-01-24 11:05:59,812] [INFO] Task started: Blastn
[2024-01-24 11:05:59,812] [INFO] Running command: blastn -query GCF_022808325.1_ASM2280832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference/reference_markers.fasta -out GCF_022808325.1_ASM2280832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:00,794] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:00,797] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:00,798] [INFO] Target genome list was writen to GCF_022808325.1_ASM2280832v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:00,805] [INFO] Task started: fastANI
[2024-01-24 11:06:00,805] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6d4b350-8c62-44c9-ab7b-8e7297387d4e/GCF_022808325.1_ASM2280832v1_genomic.fna.gz --refList GCF_022808325.1_ASM2280832v1_genomic.fna/target_genomes.txt --output GCF_022808325.1_ASM2280832v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:13,974] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:13,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:13,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:13,989] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:13,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:13,990] [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
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	86.7749	706	910	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	84.2244	614	910	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	83.0747	632	910	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	82.9901	561	910	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.563	621	910	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.4813	570	910	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.3023	614	910	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	81.8817	586	910	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	81.8553	544	910	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.8464	598	910	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.8244	556	910	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	81.7687	532	910	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	81.7672	553	910	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.7195	603	910	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	81.4524	565	910	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.2073	585	910	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	80.8494	590	910	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	80.8034	523	910	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	80.1812	495	910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,991] [INFO] DFAST Taxonomy check result was written to GCF_022808325.1_ASM2280832v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:13,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:13,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:13,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference/checkm_data
[2024-01-24 11:06:13,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:14,020] [INFO] Task started: CheckM
[2024-01-24 11:06:14,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022808325.1_ASM2280832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022808325.1_ASM2280832v1_genomic.fna/checkm_input GCF_022808325.1_ASM2280832v1_genomic.fna/checkm_result
[2024-01-24 11:06:55,889] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:55,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:55,906] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:55,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:55,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022808325.1_ASM2280832v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:55,907] [INFO] Task started: Blastn
[2024-01-24 11:06:55,907] [INFO] Running command: blastn -query GCF_022808325.1_ASM2280832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b304c4e-174a-47c1-92f2-65d299baace3/dqc_reference/reference_markers_gtdb.fasta -out GCF_022808325.1_ASM2280832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:57,865] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:57,908] [INFO] Selected 22 target genomes.
[2024-01-24 11:06:57,909] [INFO] Target genome list was writen to GCF_022808325.1_ASM2280832v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:57,923] [INFO] Task started: fastANI
[2024-01-24 11:06:57,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6d4b350-8c62-44c9-ab7b-8e7297387d4e/GCF_022808325.1_ASM2280832v1_genomic.fna.gz --refList GCF_022808325.1_ASM2280832v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022808325.1_ASM2280832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:13,368] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:13,384] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:07:13,384] [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_003416885.1	s__Luteimonas_B sp003416885	86.7749	706	910	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_006476065.1	s__Luteimonas_B lumbrici	84.2345	614	910	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_004297225.1	s__Luteimonas_B sp004297225	83.8476	543	910	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_000422305.1	s__Luteimonas mephitis	83.0645	632	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	82.9804	561	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	82.6834	592	910	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_007859325.1	s__Luteimonas marina	82.5635	621	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	82.4672	571	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	82.4146	471	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	81.9279	600	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107375.1	s__Lysobacter sp900107375	81.9152	643	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	81.869	543	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	81.8417	555	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	81.8374	599	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	81.7972	473	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	81.7876	585	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546735.2	s__Lysobacter maris	81.7076	537	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_008312895.1	s__Luteimonas sp008312895	81.6849	594	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502915.1	s__SCMT01 sp005502915	81.2063	550	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018406645.1	s__Lysobacter_A helvus	81.1138	583	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	81.0854	535	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCA_002240395.1	s__Luteimonas citri_A	80.3557	491	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:13,386] [INFO] GTDB search result was written to GCF_022808325.1_ASM2280832v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:13,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:13,391] [INFO] DFAST_QC result json was written to GCF_022808325.1_ASM2280832v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:13,391] [INFO] DFAST_QC completed!
[2024-01-24 11:07:13,391] [INFO] Total running time: 0h1m24s