[2024-01-24 13:27:46,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference
[2024-01-24 13:27:47,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,810] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f643eb2-f368-4a6b-8ab6-cd55b9eac9a8/GCF_014656335.1_ASM1465633v1_genomic.fna.gz | prodigal -d GCF_014656335.1_ASM1465633v1_genomic.fna/cds.fna -a GCF_014656335.1_ASM1465633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:57,165] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:57,165] [INFO] Task started: HMMsearch
[2024-01-24 13:27:57,166] [INFO] Running command: hmmsearch --tblout GCF_014656335.1_ASM1465633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference/reference_markers.hmm GCF_014656335.1_ASM1465633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:57,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:57,472] [INFO] Found 6/6 markers.
[2024-01-24 13:27:57,503] [INFO] Query marker FASTA was written to GCF_014656335.1_ASM1465633v1_genomic.fna/markers.fasta
[2024-01-24 13:27:57,503] [INFO] Task started: Blastn
[2024-01-24 13:27:57,503] [INFO] Running command: blastn -query GCF_014656335.1_ASM1465633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference/reference_markers.fasta -out GCF_014656335.1_ASM1465633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:58,584] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:58,588] [INFO] Selected 14 target genomes.
[2024-01-24 13:27:58,588] [INFO] Target genome list was writen to GCF_014656335.1_ASM1465633v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:58,608] [INFO] Task started: fastANI
[2024-01-24 13:27:58,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f643eb2-f368-4a6b-8ab6-cd55b9eac9a8/GCF_014656335.1_ASM1465633v1_genomic.fna.gz --refList GCF_014656335.1_ASM1465633v1_genomic.fna/target_genomes.txt --output GCF_014656335.1_ASM1465633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:11,443] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:11,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:11,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:11,456] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:11,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:11,457] [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 thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	100.0	1001	1003	95	conclusive
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	99.9496	967	1003	95	conclusive
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	83.8791	660	1003	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	83.7038	709	1003	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	83.6212	612	1003	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.0669	542	1003	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.0362	642	1003	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.9479	623	1003	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.9357	688	1003	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.7774	563	1003	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.6588	651	1003	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.5625	648	1003	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.3529	579	1003	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.1111	643	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:11,459] [INFO] DFAST Taxonomy check result was written to GCF_014656335.1_ASM1465633v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:11,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:11,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:11,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference/checkm_data
[2024-01-24 13:28:11,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:11,498] [INFO] Task started: CheckM
[2024-01-24 13:28:11,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656335.1_ASM1465633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656335.1_ASM1465633v1_genomic.fna/checkm_input GCF_014656335.1_ASM1465633v1_genomic.fna/checkm_result
[2024-01-24 13:28:57,410] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:57,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,441] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:57,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:57,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656335.1_ASM1465633v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:57,442] [INFO] Task started: Blastn
[2024-01-24 13:28:57,443] [INFO] Running command: blastn -query GCF_014656335.1_ASM1465633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309c1d27-440b-4d2e-a5cc-9cdffc75a223/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656335.1_ASM1465633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:59,716] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:59,721] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:59,721] [INFO] Target genome list was writen to GCF_014656335.1_ASM1465633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:59,776] [INFO] Task started: fastANI
[2024-01-24 13:28:59,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f643eb2-f368-4a6b-8ab6-cd55b9eac9a8/GCF_014656335.1_ASM1465633v1_genomic.fna.gz --refList GCF_014656335.1_ASM1465633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656335.1_ASM1465633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:14,843] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,861] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:14,861] [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_007923255.1	s__Lysobacter thermophilus	99.9496	967	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_003814555.1	s__Lysobacter tengchongensis	83.6817	710	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	83.6033	612	1003	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_003586305.1	s__Lysobacter tabacisoli	82.8269	671	1003	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	82.1316	652	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	82.0363	642	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	81.8387	611	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	81.7902	562	1003	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_001429785.1	s__Lysobacter sp001429785	81.7194	677	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
GCF_003382285.1	s__Lysobacter soli	81.5958	645	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCA_013362405.1	s__JABFWF01 sp013362405	81.5724	492	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	81.479	588	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	81.4492	606	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	81.44	558	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_016774335.1	s__Luteimonas sp016774335	81.1116	643	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	81.0376	633	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	80.9373	602	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	80.5395	621	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,863] [INFO] GTDB search result was written to GCF_014656335.1_ASM1465633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:14,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:14,867] [INFO] DFAST_QC result json was written to GCF_014656335.1_ASM1465633v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:14,867] [INFO] DFAST_QC completed!
[2024-01-24 13:29:14,867] [INFO] Total running time: 0h1m29s