[2024-01-24 15:27:41,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,305] [INFO] DQC Reference Directory: /var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference
[2024-01-24 15:27:43,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,881] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3570a05-2003-4aa4-a1b3-f2f21d6fac73/GCF_003697345.1_ASM369734v1_genomic.fna.gz | prodigal -d GCF_003697345.1_ASM369734v1_genomic.fna/cds.fna -a GCF_003697345.1_ASM369734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:53,441] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:53,442] [INFO] Task started: HMMsearch
[2024-01-24 15:27:53,442] [INFO] Running command: hmmsearch --tblout GCF_003697345.1_ASM369734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference/reference_markers.hmm GCF_003697345.1_ASM369734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:53,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:53,688] [INFO] Found 6/6 markers.
[2024-01-24 15:27:53,725] [INFO] Query marker FASTA was written to GCF_003697345.1_ASM369734v1_genomic.fna/markers.fasta
[2024-01-24 15:27:53,725] [INFO] Task started: Blastn
[2024-01-24 15:27:53,725] [INFO] Running command: blastn -query GCF_003697345.1_ASM369734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference/reference_markers.fasta -out GCF_003697345.1_ASM369734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,653] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,657] [INFO] Selected 21 target genomes.
[2024-01-24 15:27:54,657] [INFO] Target genome list was writen to GCF_003697345.1_ASM369734v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:54,701] [INFO] Task started: fastANI
[2024-01-24 15:27:54,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3570a05-2003-4aa4-a1b3-f2f21d6fac73/GCF_003697345.1_ASM369734v1_genomic.fna.gz --refList GCF_003697345.1_ASM369734v1_genomic.fna/target_genomes.txt --output GCF_003697345.1_ASM369734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:08,205] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:08,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:08,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:08,225] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:08,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:08,225] [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 pythonis	strain=4284/11	GCA_003697345.1	2483112	2483112	type	True	100.0	936	938	95	conclusive
Lysobacter oculi	strain=83-4	GCA_003293695.1	2698682	2698682	type	True	82.5455	572	938	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.4151	490	938	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	79.9979	454	938	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	79.9954	468	938	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	79.9632	482	938	95	below_threshold
Lysobacter tolerans	strain=UM1	GCA_900155935.1	1604334	1604334	type	True	79.943	438	938	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.8815	393	938	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	79.8473	475	938	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	79.6922	437	938	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	79.6621	454	938	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.5682	496	938	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	79.4627	441	938	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.4582	463	938	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	79.3942	422	938	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	79.3519	434	938	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	79.2923	390	938	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	79.2007	454	938	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	79.1874	437	938	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	79.1545	425	938	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	79.1274	431	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:08,227] [INFO] DFAST Taxonomy check result was written to GCF_003697345.1_ASM369734v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:08,228] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:08,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:08,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference/checkm_data
[2024-01-24 15:28:08,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:08,262] [INFO] Task started: CheckM
[2024-01-24 15:28:08,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003697345.1_ASM369734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003697345.1_ASM369734v1_genomic.fna/checkm_input GCF_003697345.1_ASM369734v1_genomic.fna/checkm_result
[2024-01-24 15:28:41,587] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:41,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:41,614] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:41,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:41,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003697345.1_ASM369734v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:41,617] [INFO] Task started: Blastn
[2024-01-24 15:28:41,617] [INFO] Running command: blastn -query GCF_003697345.1_ASM369734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb234ccea-02af-427a-bb03-527448e3bdb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003697345.1_ASM369734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:43,368] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:43,371] [INFO] Selected 21 target genomes.
[2024-01-24 15:28:43,371] [INFO] Target genome list was writen to GCF_003697345.1_ASM369734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:43,392] [INFO] Task started: fastANI
[2024-01-24 15:28:43,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3570a05-2003-4aa4-a1b3-f2f21d6fac73/GCF_003697345.1_ASM369734v1_genomic.fna.gz --refList GCF_003697345.1_ASM369734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003697345.1_ASM369734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:55,920] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:55,944] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:55,945] [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_003697345.1	s__Lysobacter_B pythonis	100.0	936	938	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
GCF_003293695.1	s__Lysobacter_B oculi	82.5873	569	938	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_014879375.1	s__Lysobacter_B sp014879375	80.9582	413	938	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	80.4391	488	938	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	80.1467	463	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_000423885.1	s__Thermomonas fusca	79.9859	455	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_900155935.1	s__Lysobacter_B tolerans	79.9504	437	938	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_000422305.1	s__Luteimonas mephitis	79.9152	453	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	79.8637	474	938	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	79.6917	437	938	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_000513955.1	s__Pseudoxanthomonas suwonensis_C	79.6003	443	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	79.4806	440	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	79.4574	466	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	79.4474	464	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239095.1	s__Luteimonas_C gilva	79.3879	423	938	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_010211745.1	s__Pseudoxanthomonas_A kalamensis	79.385	407	938	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_019218945.1	s__Pseudoxanthomonas_A sp019218945	79.2129	458	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCA_002798255.1	s__Lysobacter_B sp002798255	79.161	355	938	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_002798295.1	s__Lysobacter_B sp002798295	78.9926	376	938	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_018242405.1	s__Lysobacter_B sp018242405	78.9302	344	938	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_002798275.1	s__Lysobacter_B sp002798275	78.8559	359	938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	98.40	98.40	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:55,946] [INFO] GTDB search result was written to GCF_003697345.1_ASM369734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:55,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:55,951] [INFO] DFAST_QC result json was written to GCF_003697345.1_ASM369734v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:55,952] [INFO] DFAST_QC completed!
[2024-01-24 15:28:55,952] [INFO] Total running time: 0h1m15s