[2024-01-24 13:22:02,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference
[2024-01-24 13:22:03,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,703] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,703] [INFO] Running command: gunzip -c /var/lib/cwl/stgec4122c5-2495-448c-b06d-b1d194704516/GCF_003628435.1_ASM362843v1_genomic.fna.gz | prodigal -d GCF_003628435.1_ASM362843v1_genomic.fna/cds.fna -a GCF_003628435.1_ASM362843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:10,209] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:10,209] [INFO] Task started: HMMsearch
[2024-01-24 13:22:10,209] [INFO] Running command: hmmsearch --tblout GCF_003628435.1_ASM362843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference/reference_markers.hmm GCF_003628435.1_ASM362843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:10,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:10,562] [INFO] Found 6/6 markers.
[2024-01-24 13:22:10,594] [INFO] Query marker FASTA was written to GCF_003628435.1_ASM362843v1_genomic.fna/markers.fasta
[2024-01-24 13:22:10,594] [INFO] Task started: Blastn
[2024-01-24 13:22:10,594] [INFO] Running command: blastn -query GCF_003628435.1_ASM362843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference/reference_markers.fasta -out GCF_003628435.1_ASM362843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:11,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:11,227] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:11,227] [INFO] Target genome list was writen to GCF_003628435.1_ASM362843v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:11,234] [INFO] Task started: fastANI
[2024-01-24 13:22:11,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgec4122c5-2495-448c-b06d-b1d194704516/GCF_003628435.1_ASM362843v1_genomic.fna.gz --refList GCF_003628435.1_ASM362843v1_genomic.fna/target_genomes.txt --output GCF_003628435.1_ASM362843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:23,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:23,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:23,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:23,659] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:23,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:23,659] [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
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.2964	393	1118	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.2889	391	1118	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.9973	414	1118	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.973	412	1118	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	78.9232	325	1118	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	78.9232	325	1118	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	78.8659	307	1118	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	78.8659	307	1118	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	78.8579	345	1118	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	78.6756	331	1118	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	78.4436	228	1118	95	below_threshold
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	78.4325	235	1118	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	78.3689	232	1118	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	78.3195	234	1118	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	78.2685	239	1118	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.043	235	1118	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.4611	209	1118	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.601	71	1118	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	75.8604	61	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:23,661] [INFO] DFAST Taxonomy check result was written to GCF_003628435.1_ASM362843v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:23,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:23,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:23,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference/checkm_data
[2024-01-24 13:22:23,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:23,699] [INFO] Task started: CheckM
[2024-01-24 13:22:23,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003628435.1_ASM362843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003628435.1_ASM362843v1_genomic.fna/checkm_input GCF_003628435.1_ASM362843v1_genomic.fna/checkm_result
[2024-01-24 13:22:50,314] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:50,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:50,334] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:50,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:50,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003628435.1_ASM362843v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:50,335] [INFO] Task started: Blastn
[2024-01-24 13:22:50,335] [INFO] Running command: blastn -query GCF_003628435.1_ASM362843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d007244-7fff-4c56-938a-7fd44b189858/dqc_reference/reference_markers_gtdb.fasta -out GCF_003628435.1_ASM362843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:51,228] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:51,232] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:51,232] [INFO] Target genome list was writen to GCF_003628435.1_ASM362843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:51,252] [INFO] Task started: fastANI
[2024-01-24 13:22:51,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgec4122c5-2495-448c-b06d-b1d194704516/GCF_003628435.1_ASM362843v1_genomic.fna.gz --refList GCF_003628435.1_ASM362843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003628435.1_ASM362843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:02,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:02,155] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:02,155] [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_003628435.1	s__Ureibacillus endophyticus	99.979	1111	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900217795.1	s__Ureibacillus xyleni	85.6242	846	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977595.1	s__Ureibacillus antri	80.8742	600	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	-
GCF_003966145.1	s__Ureibacillus telephonicus	79.8023	470	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	79.5892	450	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	79.4561	430	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491425.1	s__Ureibacillus sp005491425	79.4103	410	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217295.1	s__Ureibacillus chungkukjangi	79.3034	390	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016908465.1	s__Ureibacillus composti	78.9931	410	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000772965.1	s__Ureibacillus massiliensis	78.9232	325	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900220965.1	s__Ureibacillus acetophenoni	78.8579	345	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982115.1	s__Lysinibacillus sphaericus	78.4117	235	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:02,157] [INFO] GTDB search result was written to GCF_003628435.1_ASM362843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:02,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:02,161] [INFO] DFAST_QC result json was written to GCF_003628435.1_ASM362843v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:02,162] [INFO] DFAST_QC completed!
[2024-01-24 13:23:02,162] [INFO] Total running time: 0h0m60s