[2024-01-24 10:47:06,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg73ef32f3-fef1-4f33-b120-810a2bdb1de8/GCF_003856865.1_ASM385686v1_genomic.fna.gz | prodigal -d GCF_003856865.1_ASM385686v1_genomic.fna/cds.fna -a GCF_003856865.1_ASM385686v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,407] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,407] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,407] [INFO] Running command: hmmsearch --tblout GCF_003856865.1_ASM385686v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference/reference_markers.hmm GCF_003856865.1_ASM385686v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,685] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,726] [INFO] Query marker FASTA was written to GCF_003856865.1_ASM385686v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,726] [INFO] Task started: Blastn
[2024-01-24 10:47:20,726] [INFO] Running command: blastn -query GCF_003856865.1_ASM385686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference/reference_markers.fasta -out GCF_003856865.1_ASM385686v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,341] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,345] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:21,345] [INFO] Target genome list was writen to GCF_003856865.1_ASM385686v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:21,365] [INFO] Task started: fastANI
[2024-01-24 10:47:21,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ef32f3-fef1-4f33-b120-810a2bdb1de8/GCF_003856865.1_ASM385686v1_genomic.fna.gz --refList GCF_003856865.1_ASM385686v1_genomic.fna/target_genomes.txt --output GCF_003856865.1_ASM385686v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:32,166] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:32,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:32,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:32,180] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:32,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:32,180] [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=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	100.0	1389	1392	95	conclusive
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	99.995	1367	1392	95	conclusive
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.0558	355	1392	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	79.013	356	1392	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.0023	361	1392	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.0002	357	1392	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	78.7735	355	1392	95	below_threshold
Lysinibacillus odysseyi	strain=NBRC 100172	GCA_000773015.1	202611	202611	type	True	78.5053	171	1392	95	below_threshold
Lysinibacillus odysseyi	strain=NBRC 100172	GCA_001591965.1	202611	202611	type	True	78.3408	173	1392	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.9956	227	1392	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	77.8148	214	1392	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.5685	193	1392	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.4998	77	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:32,191] [INFO] DFAST Taxonomy check result was written to GCF_003856865.1_ASM385686v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:32,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:32,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:32,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference/checkm_data
[2024-01-24 10:47:32,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:32,235] [INFO] Task started: CheckM
[2024-01-24 10:47:32,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003856865.1_ASM385686v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003856865.1_ASM385686v1_genomic.fna/checkm_input GCF_003856865.1_ASM385686v1_genomic.fna/checkm_result
[2024-01-24 10:48:02,458] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:02,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:02,480] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:02,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:02,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003856865.1_ASM385686v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:02,481] [INFO] Task started: Blastn
[2024-01-24 10:48:02,481] [INFO] Running command: blastn -query GCF_003856865.1_ASM385686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg184a09d0-1907-46b1-a29f-12da192e12a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003856865.1_ASM385686v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:03,465] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:03,468] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:03,468] [INFO] Target genome list was writen to GCF_003856865.1_ASM385686v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:03,501] [INFO] Task started: fastANI
[2024-01-24 10:48:03,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ef32f3-fef1-4f33-b120-810a2bdb1de8/GCF_003856865.1_ASM385686v1_genomic.fna.gz --refList GCF_003856865.1_ASM385686v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003856865.1_ASM385686v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:16,550] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,564] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:16,564] [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	99.995	1367	1392	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_003711845.1	s__Ureibacillus halotolerans	79.4379	354	1392	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_003966145.1	s__Ureibacillus telephonicus	79.1996	419	1392	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	79.1688	408	1392	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	79.0497	388	1392	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	79.0283	396	1392	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	79.0175	358	1392	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_900217795.1	s__Ureibacillus xyleni	79.0041	397	1392	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	79.0006	357	1392	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_014836845.1	s__Ureibacillus sp014836845	78.9941	382	1392	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	78.8042	346	1392	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_900220965.1	s__Ureibacillus acetophenoni	78.793	352	1392	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	78.4644	353	1392	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_009724685.1	s__Lysinibacillus sp009724685	77.9694	227	1392	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_000392615.1	s__Lysinibacillus sphaericus_B	77.9647	207	1392	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	77.8097	129	1392	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metalysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351785.1	s__Sporosarcina sp003351785	76.4917	54	1392	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,566] [INFO] GTDB search result was written to GCF_003856865.1_ASM385686v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:16,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:16,571] [INFO] DFAST_QC result json was written to GCF_003856865.1_ASM385686v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:16,571] [INFO] DFAST_QC completed!
[2024-01-24 10:48:16,571] [INFO] Total running time: 0h1m10s