[2024-01-24 13:40:30,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference
[2024-01-24 13:40:31,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,709] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dc1fa2d-6103-4db5-bd56-75a44ac98fe9/GCF_002200835.1_ASM220083v1_genomic.fna.gz | prodigal -d GCF_002200835.1_ASM220083v1_genomic.fna/cds.fna -a GCF_002200835.1_ASM220083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,273] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,273] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,273] [INFO] Running command: hmmsearch --tblout GCF_002200835.1_ASM220083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference/reference_markers.hmm GCF_002200835.1_ASM220083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:42,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:42,608] [INFO] Found 6/6 markers.
[2024-01-24 13:40:42,651] [INFO] Query marker FASTA was written to GCF_002200835.1_ASM220083v1_genomic.fna/markers.fasta
[2024-01-24 13:40:42,651] [INFO] Task started: Blastn
[2024-01-24 13:40:42,651] [INFO] Running command: blastn -query GCF_002200835.1_ASM220083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference/reference_markers.fasta -out GCF_002200835.1_ASM220083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:43,281] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:43,285] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:43,285] [INFO] Target genome list was writen to GCF_002200835.1_ASM220083v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:43,291] [INFO] Task started: fastANI
[2024-01-24 13:40:43,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc1fa2d-6103-4db5-bd56-75a44ac98fe9/GCF_002200835.1_ASM220083v1_genomic.fna.gz --refList GCF_002200835.1_ASM220083v1_genomic.fna/target_genomes.txt --output GCF_002200835.1_ASM220083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:55,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:55,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:55,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:55,409] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:40:55,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:55,409] [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 odysseyi	strain=NBRC 100172	GCA_000773015.1	202611	202611	type	True	100.0	1480	1482	95	conclusive
Lysinibacillus odysseyi	strain=NBRC 100172	GCA_002200835.1	202611	202611	type	True	100.0	1480	1482	95	conclusive
Lysinibacillus odysseyi	strain=NBRC 100172	GCA_001591965.1	202611	202611	type	True	99.9964	1472	1482	95	conclusive
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	78.677	219	1482	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	78.6479	226	1482	95	below_threshold
Solibacillus kalamii	strain=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	78.4609	259	1482	95	below_threshold
Solibacillus kalamii	strain=ISSFR-015	GCA_002174535.1	1748298	1748298	type	True	78.4316	257	1482	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.3922	169	1482	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	78.3561	183	1482	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.355	167	1482	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	78.3503	149	1482	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	78.3503	149	1482	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	78.2639	199	1482	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	78.1824	205	1482	95	below_threshold
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	78.1526	215	1482	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	78.0418	211	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:55,412] [INFO] DFAST Taxonomy check result was written to GCF_002200835.1_ASM220083v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:55,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:55,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:55,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference/checkm_data
[2024-01-24 13:40:55,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:55,465] [INFO] Task started: CheckM
[2024-01-24 13:40:55,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002200835.1_ASM220083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002200835.1_ASM220083v1_genomic.fna/checkm_input GCF_002200835.1_ASM220083v1_genomic.fna/checkm_result
[2024-01-24 13:41:31,418] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:31,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:31,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:31,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002200835.1_ASM220083v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:31,445] [INFO] Task started: Blastn
[2024-01-24 13:41:31,446] [INFO] Running command: blastn -query GCF_002200835.1_ASM220083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45bfac5d-d219-4c57-90dc-aeb7778e67a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002200835.1_ASM220083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,253] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,257] [INFO] Selected 24 target genomes.
[2024-01-24 13:41:32,257] [INFO] Target genome list was writen to GCF_002200835.1_ASM220083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:32,271] [INFO] Task started: fastANI
[2024-01-24 13:41:32,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc1fa2d-6103-4db5-bd56-75a44ac98fe9/GCF_002200835.1_ASM220083v1_genomic.fna.gz --refList GCF_002200835.1_ASM220083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002200835.1_ASM220083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:49,768] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:49,786] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:49,787] [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_001591965.1	s__Lysinibacillus_B odysseyi	99.9964	1472	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus_B	95.0	99.67	99.01	0.98	0.95	4	conclusive
GCA_002359075.1	s__Lysinibacillus_B sp002359075	86.0187	680	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595895.1	s__Lysinibacillus_B odysseyi_A	78.772	299	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049665.1	s__Lysinibacillus mangiferihumi	78.6771	222	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.98	99.98	0.98	0.98	2	-
GCF_000772935.1	s__Lysinibacillus boronitolerans	78.6021	189	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	99.49	98.68	0.97	0.91	4	-
GCF_003049505.1	s__Metasolibacillus meyeri	78.5453	196	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001275675.1	s__Lysinibacillus sp001275675	78.3811	197	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015999545.1	s__Lysinibacillus sp002340205	78.3732	205	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.79	97.71	0.94	0.94	5	-
GCF_016908465.1	s__Ureibacillus composti	78.355	167	1482	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_000612805.1	s__Metasolibacillus ndiopicus	78.3474	220	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836905.1	s__Solibacillus sp014836905	78.3145	241	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049645.1	s__Metasolibacillus fluoroglycofenilyticus	78.248	197	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	98.96	98.96	0.94	0.94	2	-
GCF_003049525.1	s__Lysinibacillus fusiformis	78.1641	206	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.17	95.55	0.92	0.87	32	-
GCF_002982115.1	s__Lysinibacillus sphaericus	78.1357	219	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	-
GCF_001728805.1	s__Lysinibacillus sphaericus_D	78.1165	200	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.1498	99.28	99.28	0.92	0.92	2	-
GCA_002973635.1	s__Lysinibacillus sp002973635	78.0965	185	1482	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_001281525.1	s__Lysinibacillus macroides	77.9363	187	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCA_017577605.1	s__Ureibacillus sp017577605	77.1378	83	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,788] [INFO] GTDB search result was written to GCF_002200835.1_ASM220083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:49,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:49,793] [INFO] DFAST_QC result json was written to GCF_002200835.1_ASM220083v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:49,793] [INFO] DFAST_QC completed!
[2024-01-24 13:41:49,793] [INFO] Total running time: 0h1m19s