[2024-01-24 14:05:35,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:35,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:35,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference
[2024-01-24 14:05:36,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:36,589] [INFO] Task started: Prodigal
[2024-01-24 14:05:36,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg40b90d89-9698-4b38-9dac-d9d22a0b0b32/GCF_014145325.1_ASM1414532v1_genomic.fna.gz | prodigal -d GCF_014145325.1_ASM1414532v1_genomic.fna/cds.fna -a GCF_014145325.1_ASM1414532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:47,650] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:47,650] [INFO] Task started: HMMsearch
[2024-01-24 14:05:47,650] [INFO] Running command: hmmsearch --tblout GCF_014145325.1_ASM1414532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference/reference_markers.hmm GCF_014145325.1_ASM1414532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:47,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:47,988] [INFO] Found 6/6 markers.
[2024-01-24 14:05:48,022] [INFO] Query marker FASTA was written to GCF_014145325.1_ASM1414532v1_genomic.fna/markers.fasta
[2024-01-24 14:05:48,023] [INFO] Task started: Blastn
[2024-01-24 14:05:48,023] [INFO] Running command: blastn -query GCF_014145325.1_ASM1414532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference/reference_markers.fasta -out GCF_014145325.1_ASM1414532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:48,974] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:48,977] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:48,978] [INFO] Target genome list was writen to GCF_014145325.1_ASM1414532v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:48,999] [INFO] Task started: fastANI
[2024-01-24 14:05:48,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b90d89-9698-4b38-9dac-d9d22a0b0b32/GCF_014145325.1_ASM1414532v1_genomic.fna.gz --refList GCF_014145325.1_ASM1414532v1_genomic.fna/target_genomes.txt --output GCF_014145325.1_ASM1414532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,506] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,522] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:07,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:07,522] [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 spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	100.0	1186	1189	95	conclusive
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	92.3301	950	1189	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	84.0814	748	1189	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	83.4637	800	1189	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	83.4562	830	1189	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	82.7313	762	1189	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.322	616	1189	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.9443	738	1189	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.674	581	1189	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	81.1657	591	1189	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.0621	582	1189	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.9197	642	1189	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.7226	711	1189	95	below_threshold
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	80.7109	508	1189	95	below_threshold
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	80.607	473	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,524] [INFO] DFAST Taxonomy check result was written to GCF_014145325.1_ASM1414532v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference/checkm_data
[2024-01-24 14:06:07,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,566] [INFO] Task started: CheckM
[2024-01-24 14:06:07,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145325.1_ASM1414532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145325.1_ASM1414532v1_genomic.fna/checkm_input GCF_014145325.1_ASM1414532v1_genomic.fna/checkm_result
[2024-01-24 14:07:04,638] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:04,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:04,659] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:04,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:04,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145325.1_ASM1414532v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:04,660] [INFO] Task started: Blastn
[2024-01-24 14:07:04,661] [INFO] Running command: blastn -query GCF_014145325.1_ASM1414532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a03c5fb-7351-4c9b-aa97-e2e4858b37f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145325.1_ASM1414532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:06,232] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:06,241] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:06,241] [INFO] Target genome list was writen to GCF_014145325.1_ASM1414532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:06,254] [INFO] Task started: fastANI
[2024-01-24 14:07:06,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b90d89-9698-4b38-9dac-d9d22a0b0b32/GCF_014145325.1_ASM1414532v1_genomic.fna.gz --refList GCF_014145325.1_ASM1414532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145325.1_ASM1414532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:19,664] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,683] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:19,683] [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_014145325.1	s__Lysobacter spongiae	100.0	1186	1189	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_006546775.1	s__Lysobacter aestuarii	92.3243	951	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546735.2	s__Lysobacter maris	84.0784	749	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_014145395.1	s__Lysobacter penaei	83.4717	799	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547045.1	s__Lysobacter alkalisoli	82.7578	760	1189	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	82.378	689	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000768335.1	s__Lysobacter arseniciresistens	82.3347	615	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	81.6942	646	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336385.2	s__Lysobacter antibioticus_A	81.5703	691	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107375.1	s__Lysobacter sp900107375	81.542	753	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209725.1	s__Lysobacter sp015209725	80.7037	509	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.91	96.91	0.94	0.94	2	-
GCF_016615955.1	s__Luteimonas sp016615955	80.5681	573	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCF_001431595.1	s__Stenotrophomonas acidaminiphila	80.4074	542	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	-
GCA_002798175.1	s__Luteimonas sp002798175	80.2531	552	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	80.0735	541	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,685] [INFO] GTDB search result was written to GCF_014145325.1_ASM1414532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:19,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:19,689] [INFO] DFAST_QC result json was written to GCF_014145325.1_ASM1414532v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:19,689] [INFO] DFAST_QC completed!
[2024-01-24 14:07:19,689] [INFO] Total running time: 0h1m44s