[2024-01-24 13:01:12,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference
[2024-01-24 13:01:13,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,761] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ffc27e-9e97-4a61-9d12-03e1c07ab7cf/GCF_006546735.2_ASM654673v2_genomic.fna.gz | prodigal -d GCF_006546735.2_ASM654673v2_genomic.fna/cds.fna -a GCF_006546735.2_ASM654673v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:24,291] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:24,291] [INFO] Task started: HMMsearch
[2024-01-24 13:01:24,292] [INFO] Running command: hmmsearch --tblout GCF_006546735.2_ASM654673v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference/reference_markers.hmm GCF_006546735.2_ASM654673v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:24,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:24,617] [INFO] Found 6/6 markers.
[2024-01-24 13:01:24,665] [INFO] Query marker FASTA was written to GCF_006546735.2_ASM654673v2_genomic.fna/markers.fasta
[2024-01-24 13:01:24,666] [INFO] Task started: Blastn
[2024-01-24 13:01:24,666] [INFO] Running command: blastn -query GCF_006546735.2_ASM654673v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference/reference_markers.fasta -out GCF_006546735.2_ASM654673v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:25,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:25,848] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:25,849] [INFO] Target genome list was writen to GCF_006546735.2_ASM654673v2_genomic.fna/target_genomes.txt
[2024-01-24 13:01:25,861] [INFO] Task started: fastANI
[2024-01-24 13:01:25,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ffc27e-9e97-4a61-9d12-03e1c07ab7cf/GCF_006546735.2_ASM654673v2_genomic.fna.gz --refList GCF_006546735.2_ASM654673v2_genomic.fna/target_genomes.txt --output GCF_006546735.2_ASM654673v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:41,488] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:41,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:41,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:41,501] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:41,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:41,502] [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 maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	100.0	1196	1207	95	conclusive
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	87.4386	925	1207	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	84.6544	769	1207	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	83.8782	746	1207	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	83.8332	709	1207	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	83.2555	653	1207	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	83.148	591	1207	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.3967	736	1207	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.0345	657	1207	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.9645	558	1207	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.5378	717	1207	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.4939	627	1207	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.4393	561	1207	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.4365	584	1207	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	80.752	511	1207	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	80.7438	601	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,508] [INFO] DFAST Taxonomy check result was written to GCF_006546735.2_ASM654673v2_genomic.fna/tc_result.tsv
[2024-01-24 13:01:41,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:41,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:41,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference/checkm_data
[2024-01-24 13:01:41,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:41,551] [INFO] Task started: CheckM
[2024-01-24 13:01:41,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006546735.2_ASM654673v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006546735.2_ASM654673v2_genomic.fna/checkm_input GCF_006546735.2_ASM654673v2_genomic.fna/checkm_result
[2024-01-24 13:02:16,962] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:16,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:16,985] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:16,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:16,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006546735.2_ASM654673v2_genomic.fna/markers.fasta)
[2024-01-24 13:02:16,986] [INFO] Task started: Blastn
[2024-01-24 13:02:16,986] [INFO] Running command: blastn -query GCF_006546735.2_ASM654673v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c39f5a-d7b9-45ed-9ec2-633998754d03/dqc_reference/reference_markers_gtdb.fasta -out GCF_006546735.2_ASM654673v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:18,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:18,923] [INFO] Selected 13 target genomes.
[2024-01-24 13:02:18,923] [INFO] Target genome list was writen to GCF_006546735.2_ASM654673v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:18,931] [INFO] Task started: fastANI
[2024-01-24 13:02:18,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ffc27e-9e97-4a61-9d12-03e1c07ab7cf/GCF_006546735.2_ASM654673v2_genomic.fna.gz --refList GCF_006546735.2_ASM654673v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006546735.2_ASM654673v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:29,164] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:29,176] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:29,176] [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_006546735.2	s__Lysobacter maris	100.0	1196	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	conclusive
GCF_006547045.1	s__Lysobacter alkalisoli	84.6645	768	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145325.1	s__Lysobacter spongiae	83.8567	748	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546775.1	s__Lysobacter aestuarii	83.8358	709	1207	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	83.2689	652	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	83.1044	594	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	82.6366	626	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382365.1	s__Lysobacter silvisoli	82.3961	735	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	82.0704	547	1207	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_007859325.1	s__Luteimonas marina	82.0344	657	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.5009	556	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	80.8046	419	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613535.2	s__Lysobacter solisilvae_A	80.7343	602	1207	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 13:02:29,178] [INFO] GTDB search result was written to GCF_006546735.2_ASM654673v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:29,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:29,183] [INFO] DFAST_QC result json was written to GCF_006546735.2_ASM654673v2_genomic.fna/dqc_result.json
[2024-01-24 13:02:29,184] [INFO] DFAST_QC completed!
[2024-01-24 13:02:29,184] [INFO] Total running time: 0h1m17s