[2024-01-24 14:06:05,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference
[2024-01-24 14:06:07,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,056] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,056] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f5a5c1f-177e-4b62-add6-7f989132ef07/GCF_014652095.1_ASM1465209v1_genomic.fna.gz | prodigal -d GCF_014652095.1_ASM1465209v1_genomic.fna/cds.fna -a GCF_014652095.1_ASM1465209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:18,140] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:18,141] [INFO] Task started: HMMsearch
[2024-01-24 14:06:18,141] [INFO] Running command: hmmsearch --tblout GCF_014652095.1_ASM1465209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference/reference_markers.hmm GCF_014652095.1_ASM1465209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:18,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:18,467] [INFO] Found 6/6 markers.
[2024-01-24 14:06:18,498] [INFO] Query marker FASTA was written to GCF_014652095.1_ASM1465209v1_genomic.fna/markers.fasta
[2024-01-24 14:06:18,498] [INFO] Task started: Blastn
[2024-01-24 14:06:18,498] [INFO] Running command: blastn -query GCF_014652095.1_ASM1465209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference/reference_markers.fasta -out GCF_014652095.1_ASM1465209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,455] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,458] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:19,459] [INFO] Target genome list was writen to GCF_014652095.1_ASM1465209v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:19,473] [INFO] Task started: fastANI
[2024-01-24 14:06:19,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5a5c1f-177e-4b62-add6-7f989132ef07/GCF_014652095.1_ASM1465209v1_genomic.fna.gz --refList GCF_014652095.1_ASM1465209v1_genomic.fna/target_genomes.txt --output GCF_014652095.1_ASM1465209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:39,801] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:39,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:39,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:39,820] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:39,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:39,820] [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 bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	100.0	1143	1145	95	conclusive
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	81.3031	575	1145	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	81.1791	600	1145	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	80.8635	582	1145	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	80.843	590	1145	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.8334	597	1145	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.7802	630	1145	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.7646	584	1145	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	80.5488	559	1145	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	80.4665	585	1145	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	80.4326	575	1145	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	80.2437	536	1145	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.1151	569	1145	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	80.0967	506	1145	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	79.9998	535	1145	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	79.963	567	1145	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	79.9586	460	1145	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	79.9449	624	1145	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	79.8999	580	1145	95	below_threshold
Lysobacter concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	79.7918	502	1145	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	79.6294	474	1145	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	79.615	494	1145	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	78.9664	455	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:39,822] [INFO] DFAST Taxonomy check result was written to GCF_014652095.1_ASM1465209v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:39,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:39,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:39,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference/checkm_data
[2024-01-24 14:06:39,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:39,861] [INFO] Task started: CheckM
[2024-01-24 14:06:39,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652095.1_ASM1465209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652095.1_ASM1465209v1_genomic.fna/checkm_input GCF_014652095.1_ASM1465209v1_genomic.fna/checkm_result
[2024-01-24 14:07:22,192] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:22,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:22,214] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:22,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:22,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652095.1_ASM1465209v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:22,215] [INFO] Task started: Blastn
[2024-01-24 14:07:22,216] [INFO] Running command: blastn -query GCF_014652095.1_ASM1465209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c06af3e-6734-42cc-b372-078ec5a46f73/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652095.1_ASM1465209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:24,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:24,046] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:24,047] [INFO] Target genome list was writen to GCF_014652095.1_ASM1465209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:24,061] [INFO] Task started: fastANI
[2024-01-24 14:07:24,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5a5c1f-177e-4b62-add6-7f989132ef07/GCF_014652095.1_ASM1465209v1_genomic.fna.gz --refList GCF_014652095.1_ASM1465209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652095.1_ASM1465209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:38,093] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:38,113] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:38,113] [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_014652095.1	s__Lysobacter bugurensis	100.0	1143	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003586305.1	s__Lysobacter tabacisoli	81.6147	652	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805755.1	s__Lysobacter sp902805755	81.2874	410	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359965.1	s__Lysobacter segetis	81.257	579	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651995.1	s__Lysobacter xinjiangensis	81.192	598	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	80.9533	583	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382285.1	s__Lysobacter soli	80.8374	591	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_000768335.1	s__Lysobacter arseniciresistens	80.7645	584	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	80.7507	633	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015453285.1	s__Lysobacter niastensis	80.5269	561	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735495.2	s__Lysobacter sp016735495	80.5255	588	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	80.4201	577	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCA_001830245.1	s__Lysobacter sp001830245	80.304	543	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_907164845.1	s__Lysobacter sp907164845	80.212	539	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	80.166	599	1145	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	80.1283	629	1145	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	80.0082	506	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731095.1	s__Lysobacter antibioticus_B	79.9988	570	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145395.1	s__Lysobacter penaei	79.9472	461	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,115] [INFO] GTDB search result was written to GCF_014652095.1_ASM1465209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:38,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:38,119] [INFO] DFAST_QC result json was written to GCF_014652095.1_ASM1465209v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:38,120] [INFO] DFAST_QC completed!
[2024-01-24 14:07:38,120] [INFO] Total running time: 0h1m32s