[2024-01-24 11:50:49,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference
[2024-01-24 11:50:51,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:51,002] [INFO] Task started: Prodigal
[2024-01-24 11:50:51,002] [INFO] Running command: gunzip -c /var/lib/cwl/stged9ec7bb-29ca-4396-a3d4-489e707278c2/GCF_016908465.1_ASM1690846v1_genomic.fna.gz | prodigal -d GCF_016908465.1_ASM1690846v1_genomic.fna/cds.fna -a GCF_016908465.1_ASM1690846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:50:59,026] [INFO] Task succeeded: Prodigal
[2024-01-24 11:50:59,026] [INFO] Task started: HMMsearch
[2024-01-24 11:50:59,027] [INFO] Running command: hmmsearch --tblout GCF_016908465.1_ASM1690846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference/reference_markers.hmm GCF_016908465.1_ASM1690846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:50:59,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:50:59,300] [INFO] Found 6/6 markers.
[2024-01-24 11:50:59,337] [INFO] Query marker FASTA was written to GCF_016908465.1_ASM1690846v1_genomic.fna/markers.fasta
[2024-01-24 11:50:59,337] [INFO] Task started: Blastn
[2024-01-24 11:50:59,337] [INFO] Running command: blastn -query GCF_016908465.1_ASM1690846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference/reference_markers.fasta -out GCF_016908465.1_ASM1690846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:50:59,973] [INFO] Task succeeded: Blastn
[2024-01-24 11:50:59,977] [INFO] Selected 14 target genomes.
[2024-01-24 11:50:59,978] [INFO] Target genome list was writen to GCF_016908465.1_ASM1690846v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:00,693] [INFO] Task started: fastANI
[2024-01-24 11:51:00,694] [INFO] Running command: fastANI --query /var/lib/cwl/stged9ec7bb-29ca-4396-a3d4-489e707278c2/GCF_016908465.1_ASM1690846v1_genomic.fna.gz --refList GCF_016908465.1_ASM1690846v1_genomic.fna/target_genomes.txt --output GCF_016908465.1_ASM1690846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:10,855] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:10,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:10,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:10,879] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:10,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:10,880] [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
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	100.0	1388	1391	95	conclusive
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	99.9983	1389	1391	95	conclusive
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	79.1107	354	1391	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.1105	354	1391	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	78.8731	358	1391	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	78.8459	357	1391	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	78.6977	358	1391	95	below_threshold
Lysinibacillus odysseyi	strain=NBRC 100172	GCA_000773015.1	202611	202611	type	True	78.5062	172	1391	95	below_threshold
Lysinibacillus odysseyi	strain=NBRC 100172	GCA_001591965.1	202611	202611	type	True	78.3179	173	1391	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.8369	225	1391	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	77.7902	212	1391	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.5647	204	1391	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.6104	78	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:10,881] [INFO] DFAST Taxonomy check result was written to GCF_016908465.1_ASM1690846v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:10,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:10,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:10,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference/checkm_data
[2024-01-24 11:51:10,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:10,931] [INFO] Task started: CheckM
[2024-01-24 11:51:10,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908465.1_ASM1690846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908465.1_ASM1690846v1_genomic.fna/checkm_input GCF_016908465.1_ASM1690846v1_genomic.fna/checkm_result
[2024-01-24 11:51:40,823] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:40,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:40,848] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:40,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:40,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908465.1_ASM1690846v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:40,850] [INFO] Task started: Blastn
[2024-01-24 11:51:40,850] [INFO] Running command: blastn -query GCF_016908465.1_ASM1690846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ade72ac-0292-4341-9fe7-be3c7cc2d345/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908465.1_ASM1690846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:41,615] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:41,619] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:41,619] [INFO] Target genome list was writen to GCF_016908465.1_ASM1690846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:41,630] [INFO] Task started: fastANI
[2024-01-24 11:51:41,631] [INFO] Running command: fastANI --query /var/lib/cwl/stged9ec7bb-29ca-4396-a3d4-489e707278c2/GCF_016908465.1_ASM1690846v1_genomic.fna.gz --refList GCF_016908465.1_ASM1690846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908465.1_ASM1690846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:54,507] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:54,527] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:54,527] [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_016908465.1	s__Ureibacillus composti	100.0	1388	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003966145.1	s__Ureibacillus telephonicus	79.243	411	1391	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	79.2124	371	1391	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_000772965.1	s__Ureibacillus massiliensis	79.1103	354	1391	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_900217795.1	s__Ureibacillus xyleni	79.0761	388	1391	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_003628435.1	s__Ureibacillus endophyticus	79.05	402	1391	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	79.0066	381	1391	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	78.9884	380	1391	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	78.906	401	1391	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_003217295.1	s__Ureibacillus chungkukjangi	78.8785	357	1391	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_900220965.1	s__Ureibacillus acetophenoni	78.6926	358	1391	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_900291985.1	s__Ureibacillus timonensis	78.6505	342	1391	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_000772945.1	s__Ureibacillus manganicus	78.4841	357	1391	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_000392615.1	s__Lysinibacillus sphaericus_B	77.9261	205	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009724685.1	s__Lysinibacillus sp009724685	77.8265	224	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643595.1	s__Metalysinibacillus alkalisoli	77.6871	128	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metalysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:54,529] [INFO] GTDB search result was written to GCF_016908465.1_ASM1690846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:54,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:54,535] [INFO] DFAST_QC result json was written to GCF_016908465.1_ASM1690846v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:54,536] [INFO] DFAST_QC completed!
[2024-01-24 11:51:54,536] [INFO] Total running time: 0h1m5s