[2024-01-24 13:13:10,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:10,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:10,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference
[2024-01-24 13:13:11,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:11,682] [INFO] Task started: Prodigal
[2024-01-24 13:13:11,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg921ad4e9-054a-4983-af6a-27e84f0ce5a0/GCF_011320095.1_ASM1132009v1_genomic.fna.gz | prodigal -d GCF_011320095.1_ASM1132009v1_genomic.fna/cds.fna -a GCF_011320095.1_ASM1132009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:20,788] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:20,789] [INFO] Task started: HMMsearch
[2024-01-24 13:13:20,789] [INFO] Running command: hmmsearch --tblout GCF_011320095.1_ASM1132009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference/reference_markers.hmm GCF_011320095.1_ASM1132009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:21,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:21,053] [INFO] Found 6/6 markers.
[2024-01-24 13:13:21,089] [INFO] Query marker FASTA was written to GCF_011320095.1_ASM1132009v1_genomic.fna/markers.fasta
[2024-01-24 13:13:21,089] [INFO] Task started: Blastn
[2024-01-24 13:13:21,089] [INFO] Running command: blastn -query GCF_011320095.1_ASM1132009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference/reference_markers.fasta -out GCF_011320095.1_ASM1132009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:22,218] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:22,221] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:22,222] [INFO] Target genome list was writen to GCF_011320095.1_ASM1132009v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:22,677] [INFO] Task started: fastANI
[2024-01-24 13:13:22,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg921ad4e9-054a-4983-af6a-27e84f0ce5a0/GCF_011320095.1_ASM1132009v1_genomic.fna.gz --refList GCF_011320095.1_ASM1132009v1_genomic.fna/target_genomes.txt --output GCF_011320095.1_ASM1132009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:38,054] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:38,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:38,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:38,072] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:38,073] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:38,073] [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	82.96	577	895	95	below_threshold
Lysobacter profundi	strain=CHu50b-3-2	GCA_009792795.1	2594501	2594501	type	True	82.2991	607	895	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.9409	520	895	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.7858	556	895	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.7192	501	895	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.5735	531	895	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.543	544	895	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.4084	508	895	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.2707	492	895	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	81.1227	523	895	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.0759	511	895	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.9898	516	895	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.9491	532	895	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.9096	486	895	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	80.8017	505	895	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	80.785	433	895	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.7348	503	895	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.5984	545	895	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	80.5936	493	895	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	80.457	474	895	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	80.1029	430	895	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,074] [INFO] DFAST Taxonomy check result was written to GCF_011320095.1_ASM1132009v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:38,075] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:38,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:38,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference/checkm_data
[2024-01-24 13:13:38,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:38,108] [INFO] Task started: CheckM
[2024-01-24 13:13:38,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011320095.1_ASM1132009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011320095.1_ASM1132009v1_genomic.fna/checkm_input GCF_011320095.1_ASM1132009v1_genomic.fna/checkm_result
[2024-01-24 13:14:12,132] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:12,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:12,146] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:12,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:12,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011320095.1_ASM1132009v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:12,147] [INFO] Task started: Blastn
[2024-01-24 13:14:12,147] [INFO] Running command: blastn -query GCF_011320095.1_ASM1132009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbceefc4-c237-4d6a-8db2-c0247b3d3eef/dqc_reference/reference_markers_gtdb.fasta -out GCF_011320095.1_ASM1132009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:14,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:14,276] [INFO] Selected 19 target genomes.
[2024-01-24 13:14:14,276] [INFO] Target genome list was writen to GCF_011320095.1_ASM1132009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:14,307] [INFO] Task started: fastANI
[2024-01-24 13:14:14,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg921ad4e9-054a-4983-af6a-27e84f0ce5a0/GCF_011320095.1_ASM1132009v1_genomic.fna.gz --refList GCF_011320095.1_ASM1132009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011320095.1_ASM1132009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:27,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:27,228] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:27,229] [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_011320095.1	s__Luteimonas_B telluris	100.0	892	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003416885.1	s__Luteimonas_B sp003416885	82.9774	576	895	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_009792795.1	s__Luteimonas_B profundi	82.2864	608	895	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	82.0558	475	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476065.1	s__Luteimonas_B lumbrici	81.9454	520	895	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	81.8084	462	895	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	81.7596	558	895	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	81.6839	504	895	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_007859325.1	s__Luteimonas marina	81.5301	534	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	81.3427	535	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.3076	489	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	81.2209	523	895	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_007830035.1	s__Luteimonas_C cucumeris	81.1373	522	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613475.2	s__Lysobacter arenosi	81.0125	515	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	80.9682	576	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCA_013361435.1	s__Lysobacter sp013361435	80.9162	494	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	80.9097	486	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	80.7431	502	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	80.4906	475	895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:27,233] [INFO] GTDB search result was written to GCF_011320095.1_ASM1132009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:27,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:27,241] [INFO] DFAST_QC result json was written to GCF_011320095.1_ASM1132009v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:27,242] [INFO] DFAST_QC completed!
[2024-01-24 13:14:27,242] [INFO] Total running time: 0h1m17s