[2024-01-25 19:10:05,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:05,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:05,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference
[2024-01-25 19:10:06,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:06,640] [INFO] Task started: Prodigal
[2024-01-25 19:10:06,640] [INFO] Running command: gunzip -c /var/lib/cwl/stge0677c07-6546-460b-9ec4-922d1cf6deb7/GCF_014836935.1_ASM1483693v1_genomic.fna.gz | prodigal -d GCF_014836935.1_ASM1483693v1_genomic.fna/cds.fna -a GCF_014836935.1_ASM1483693v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:13,313] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:13,314] [INFO] Task started: HMMsearch
[2024-01-25 19:10:13,314] [INFO] Running command: hmmsearch --tblout GCF_014836935.1_ASM1483693v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference/reference_markers.hmm GCF_014836935.1_ASM1483693v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:13,539] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:13,540] [INFO] Found 6/6 markers.
[2024-01-25 19:10:13,570] [INFO] Query marker FASTA was written to GCF_014836935.1_ASM1483693v1_genomic.fna/markers.fasta
[2024-01-25 19:10:13,570] [INFO] Task started: Blastn
[2024-01-25 19:10:13,570] [INFO] Running command: blastn -query GCF_014836935.1_ASM1483693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference/reference_markers.fasta -out GCF_014836935.1_ASM1483693v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:14,132] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:14,136] [INFO] Selected 14 target genomes.
[2024-01-25 19:10:14,136] [INFO] Target genome list was writen to GCF_014836935.1_ASM1483693v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:14,149] [INFO] Task started: fastANI
[2024-01-25 19:10:14,149] [INFO] Running command: fastANI --query /var/lib/cwl/stge0677c07-6546-460b-9ec4-922d1cf6deb7/GCF_014836935.1_ASM1483693v1_genomic.fna.gz --refList GCF_014836935.1_ASM1483693v1_genomic.fna/target_genomes.txt --output GCF_014836935.1_ASM1483693v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:25,037] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:25,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:25,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:25,045] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:25,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:25,046] [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 merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	100.0	1238	1238	95	conclusive
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	91.9704	1087	1238	95	below_threshold
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	82.6605	778	1238	95	below_threshold
Solibacillus kalamii	strain=ISSFR-015	GCA_002174535.1	1748298	1748298	type	True	82.6332	794	1238	95	below_threshold
Solibacillus kalamii	strain=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	82.5329	805	1238	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	79.0797	209	1238	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	78.3847	177	1238	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	78.3135	212	1238	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.287	208	1238	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.9987	178	1238	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.5441	157	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:25,047] [INFO] DFAST Taxonomy check result was written to GCF_014836935.1_ASM1483693v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:25,047] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:25,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:25,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference/checkm_data
[2024-01-25 19:10:25,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:25,087] [INFO] Task started: CheckM
[2024-01-25 19:10:25,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836935.1_ASM1483693v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836935.1_ASM1483693v1_genomic.fna/checkm_input GCF_014836935.1_ASM1483693v1_genomic.fna/checkm_result
[2024-01-25 19:10:50,159] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:50,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:50,179] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:50,179] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:50,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836935.1_ASM1483693v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:50,179] [INFO] Task started: Blastn
[2024-01-25 19:10:50,179] [INFO] Running command: blastn -query GCF_014836935.1_ASM1483693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg197e6b1b-4cd1-441d-87b9-9a45c960aedf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836935.1_ASM1483693v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:50,968] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:50,972] [INFO] Selected 12 target genomes.
[2024-01-25 19:10:50,972] [INFO] Target genome list was writen to GCF_014836935.1_ASM1483693v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:50,987] [INFO] Task started: fastANI
[2024-01-25 19:10:50,987] [INFO] Running command: fastANI --query /var/lib/cwl/stge0677c07-6546-460b-9ec4-922d1cf6deb7/GCF_014836935.1_ASM1483693v1_genomic.fna.gz --refList GCF_014836935.1_ASM1483693v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836935.1_ASM1483693v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:00,965] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:00,972] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:00,972] [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_014836935.1	s__Solibacillus sp014836935	100.0	1238	1238	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_014836905.1	s__Solibacillus sp014836905	91.9692	1087	1238	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	82.6976	789	1238	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_900168685.1	s__Solibacillus isronensis_A	82.5739	757	1238	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_003073375.1	s__Solibacillus sp003073375	80.4982	535	1238	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_001700315.1	s__Caryophanon tenue	79.0797	209	1238	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Caryophanon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000392615.1	s__Lysinibacillus sphaericus_B	78.4303	211	1238	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_003049575.1	s__Lysinibacillus parviboronicapiens	78.3144	212	1238	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.01	98.61	0.95	0.92	4	-
GCA_018065935.1	s__Kurthia sp018065935	78.0814	119	1238	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:00,973] [INFO] GTDB search result was written to GCF_014836935.1_ASM1483693v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:00,974] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:00,976] [INFO] DFAST_QC result json was written to GCF_014836935.1_ASM1483693v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:00,976] [INFO] DFAST_QC completed!
[2024-01-25 19:11:00,976] [INFO] Total running time: 0h0m55s