[2024-01-24 11:44:23,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference
[2024-01-24 11:44:26,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,342] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,343] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcbfe105-840f-49cb-8a7f-2370e0fbf16f/GCF_014836905.1_ASM1483690v1_genomic.fna.gz | prodigal -d GCF_014836905.1_ASM1483690v1_genomic.fna/cds.fna -a GCF_014836905.1_ASM1483690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:34,203] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:34,203] [INFO] Task started: HMMsearch
[2024-01-24 11:44:34,204] [INFO] Running command: hmmsearch --tblout GCF_014836905.1_ASM1483690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference/reference_markers.hmm GCF_014836905.1_ASM1483690v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,503] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,538] [INFO] Query marker FASTA was written to GCF_014836905.1_ASM1483690v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,539] [INFO] Task started: Blastn
[2024-01-24 11:44:34,539] [INFO] Running command: blastn -query GCF_014836905.1_ASM1483690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference/reference_markers.fasta -out GCF_014836905.1_ASM1483690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,146] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,149] [INFO] Selected 11 target genomes.
[2024-01-24 11:44:35,150] [INFO] Target genome list was writen to GCF_014836905.1_ASM1483690v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:35,168] [INFO] Task started: fastANI
[2024-01-24 11:44:35,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcbfe105-840f-49cb-8a7f-2370e0fbf16f/GCF_014836905.1_ASM1483690v1_genomic.fna.gz --refList GCF_014836905.1_ASM1483690v1_genomic.fna/target_genomes.txt --output GCF_014836905.1_ASM1483690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:43,894] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:43,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:43,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:43,914] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:43,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:43,914] [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
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	100.0	1257	1260	95	conclusive
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	91.9893	1074	1260	95	below_threshold
Solibacillus kalamii	strain=ISSFR-015	GCA_002174535.1	1748298	1748298	type	True	82.8402	757	1260	95	below_threshold
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	82.7857	783	1260	95	below_threshold
Solibacillus kalamii	strain=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	82.7104	778	1260	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	78.3926	184	1260	95	below_threshold
Lysinibacillus fusiformis	strain=NRRL NRS-350	GCA_003367495.1	28031	28031	type	True	78.3771	187	1260	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	78.3577	192	1260	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.2556	201	1260	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	78.0499	180	1260	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.6988	150	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:43,916] [INFO] DFAST Taxonomy check result was written to GCF_014836905.1_ASM1483690v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:43,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:43,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:43,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference/checkm_data
[2024-01-24 11:44:43,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:43,957] [INFO] Task started: CheckM
[2024-01-24 11:44:43,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836905.1_ASM1483690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836905.1_ASM1483690v1_genomic.fna/checkm_input GCF_014836905.1_ASM1483690v1_genomic.fna/checkm_result
[2024-01-24 11:45:12,711] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:12,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:12,731] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:12,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:12,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836905.1_ASM1483690v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:12,733] [INFO] Task started: Blastn
[2024-01-24 11:45:12,733] [INFO] Running command: blastn -query GCF_014836905.1_ASM1483690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ab6f302-61e8-4602-9a5a-bacc9664735b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836905.1_ASM1483690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:13,519] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:13,523] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:13,523] [INFO] Target genome list was writen to GCF_014836905.1_ASM1483690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:13,534] [INFO] Task started: fastANI
[2024-01-24 11:45:13,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcbfe105-840f-49cb-8a7f-2370e0fbf16f/GCF_014836905.1_ASM1483690v1_genomic.fna.gz --refList GCF_014836905.1_ASM1483690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836905.1_ASM1483690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:22,380] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:22,392] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:22,392] [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_014836905.1	s__Solibacillus sp014836905	100.0	1257	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014836935.1	s__Solibacillus sp014836935	91.9803	1075	1260	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_900168685.1	s__Solibacillus isronensis_A	82.8895	772	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001586195.1	s__Solibacillus silvestris	82.7432	797	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	98.10	97.06	0.93	0.90	6	-
GCF_003073375.1	s__Solibacillus sp003073375	80.4487	530	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003049525.1	s__Lysinibacillus fusiformis	78.3674	194	1260	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_003217295.1	s__Ureibacillus chungkukjangi	78.1436	195	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018065935.1	s__Kurthia sp018065935	77.8718	130	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:22,394] [INFO] GTDB search result was written to GCF_014836905.1_ASM1483690v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:22,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:22,398] [INFO] DFAST_QC result json was written to GCF_014836905.1_ASM1483690v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:22,398] [INFO] DFAST_QC completed!
[2024-01-24 11:45:22,398] [INFO] Total running time: 0h0m59s