[2024-01-24 13:31:57,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,520] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference
[2024-01-24 13:31:58,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,813] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg30caacdb-d294-4a92-8dcf-cbe5a6233456/GCF_014202935.1_ASM1420293v1_genomic.fna.gz | prodigal -d GCF_014202935.1_ASM1420293v1_genomic.fna/cds.fna -a GCF_014202935.1_ASM1420293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:07,132] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:07,132] [INFO] Task started: HMMsearch
[2024-01-24 13:32:07,132] [INFO] Running command: hmmsearch --tblout GCF_014202935.1_ASM1420293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference/reference_markers.hmm GCF_014202935.1_ASM1420293v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:07,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:07,353] [INFO] Found 6/6 markers.
[2024-01-24 13:32:07,378] [INFO] Query marker FASTA was written to GCF_014202935.1_ASM1420293v1_genomic.fna/markers.fasta
[2024-01-24 13:32:07,378] [INFO] Task started: Blastn
[2024-01-24 13:32:07,378] [INFO] Running command: blastn -query GCF_014202935.1_ASM1420293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference/reference_markers.fasta -out GCF_014202935.1_ASM1420293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:08,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:08,379] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:08,380] [INFO] Target genome list was writen to GCF_014202935.1_ASM1420293v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:08,388] [INFO] Task started: fastANI
[2024-01-24 13:32:08,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg30caacdb-d294-4a92-8dcf-cbe5a6233456/GCF_014202935.1_ASM1420293v1_genomic.fna.gz --refList GCF_014202935.1_ASM1420293v1_genomic.fna/target_genomes.txt --output GCF_014202935.1_ASM1420293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:25,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:25,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:25,150] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:25,150] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:25,151] [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
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.7848	527	947	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	81.5845	571	947	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	81.5777	542	947	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	81.4039	578	947	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	81.3999	537	947	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	81.1456	507	947	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	81.0789	498	947	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	81.0464	570	947	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	81.0239	540	947	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.9672	531	947	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.9114	523	947	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	80.8504	533	947	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	80.7856	543	947	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	80.7005	449	947	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.5078	495	947	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	80.4381	534	947	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.354	537	947	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.2936	487	947	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	80.273	470	947	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	80.0855	522	947	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	80.0035	533	947	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	79.9902	476	947	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	79.548	489	947	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	79.5478	488	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,152] [INFO] DFAST Taxonomy check result was written to GCF_014202935.1_ASM1420293v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:25,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:25,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:25,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference/checkm_data
[2024-01-24 13:32:25,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:25,183] [INFO] Task started: CheckM
[2024-01-24 13:32:25,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202935.1_ASM1420293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202935.1_ASM1420293v1_genomic.fna/checkm_input GCF_014202935.1_ASM1420293v1_genomic.fna/checkm_result
[2024-01-24 13:33:10,938] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:10,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,960] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:10,960] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:10,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202935.1_ASM1420293v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:10,961] [INFO] Task started: Blastn
[2024-01-24 13:33:10,961] [INFO] Running command: blastn -query GCF_014202935.1_ASM1420293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe538b1d-007a-42ab-a77c-b5d071c1f57f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202935.1_ASM1420293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:13,145] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:13,147] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:13,148] [INFO] Target genome list was writen to GCF_014202935.1_ASM1420293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:13,173] [INFO] Task started: fastANI
[2024-01-24 13:33:13,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg30caacdb-d294-4a92-8dcf-cbe5a6233456/GCF_014202935.1_ASM1420293v1_genomic.fna.gz --refList GCF_014202935.1_ASM1420293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202935.1_ASM1420293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:31,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:31,993] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:31,994] [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_014202935.1	s__Rehaibacterium terrae	100.0	947	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	81.7984	526	947	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_001724815.1	s__Arenimonas sp001724815	81.5971	565	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	81.5968	570	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	81.3973	579	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000747075.1	s__Arenimonas malthae	81.3882	539	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	81.2147	503	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_006265115.1	s__Arenimonas terrae	81.0461	570	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	81.0023	505	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	80.9149	542	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017755.1	s__VRTS01 sp008017755	80.9115	523	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__VRTS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	80.8606	539	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_000513995.1	s__Pseudoxanthomonas sp000513995	80.8196	542	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	80.8099	540	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305095.1	s__Thermomonas sp017305095	80.6686	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_014652935.1	s__Luteimonas padinae	80.5239	494	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_000743535.1	s__Arenimonas donghaensis	80.4918	523	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643775.1	s__Arenimonas soli	80.4583	532	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	80.4216	418	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	80.3298	573	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	80.264	470	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101825.1	s__Aquimonas voraii	79.9283	499	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Aquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	79.826	495	947	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_018240435.1	s__SZAS-103 sp018240435	79.5629	435	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014946745.1	s__Aquimonas sp014946745	79.3119	493	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Aquimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:31,995] [INFO] GTDB search result was written to GCF_014202935.1_ASM1420293v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:31,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:32,000] [INFO] DFAST_QC result json was written to GCF_014202935.1_ASM1420293v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:32,001] [INFO] DFAST_QC completed!
[2024-01-24 13:33:32,001] [INFO] Total running time: 0h1m34s