[2024-01-25 18:59:05,521] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:05,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:05,522] [INFO] DQC Reference Directory: /var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference
[2024-01-25 18:59:06,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:06,612] [INFO] Task started: Prodigal
[2024-01-25 18:59:06,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg158b9102-6a7f-4eac-8314-d943960efc79/GCF_014646635.1_ASM1464663v1_genomic.fna.gz | prodigal -d GCF_014646635.1_ASM1464663v1_genomic.fna/cds.fna -a GCF_014646635.1_ASM1464663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:14,203] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:14,203] [INFO] Task started: HMMsearch
[2024-01-25 18:59:14,203] [INFO] Running command: hmmsearch --tblout GCF_014646635.1_ASM1464663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference/reference_markers.hmm GCF_014646635.1_ASM1464663v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:14,431] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:14,432] [INFO] Found 6/6 markers.
[2024-01-25 18:59:14,462] [INFO] Query marker FASTA was written to GCF_014646635.1_ASM1464663v1_genomic.fna/markers.fasta
[2024-01-25 18:59:14,462] [INFO] Task started: Blastn
[2024-01-25 18:59:14,462] [INFO] Running command: blastn -query GCF_014646635.1_ASM1464663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference/reference_markers.fasta -out GCF_014646635.1_ASM1464663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:15,021] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:15,024] [INFO] Selected 18 target genomes.
[2024-01-25 18:59:15,024] [INFO] Target genome list was writen to GCF_014646635.1_ASM1464663v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:15,030] [INFO] Task started: fastANI
[2024-01-25 18:59:15,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg158b9102-6a7f-4eac-8314-d943960efc79/GCF_014646635.1_ASM1464663v1_genomic.fna.gz --refList GCF_014646635.1_ASM1464663v1_genomic.fna/target_genomes.txt --output GCF_014646635.1_ASM1464663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:29,439] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:29,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:29,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:29,448] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:59:29,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:29,448] [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
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	100.0	1140	1147	95	conclusive
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	81.5004	690	1147	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	79.3832	443	1147	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	78.2023	391	1147	95	below_threshold
Lentibacillus persicus	strain=DSM 22530	GCA_900112705.1	640948	640948	type	True	77.8415	291	1147	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.4464	107	1147	95	below_threshold
Lentibacillus cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	77.2139	196	1147	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.1932	127	1147	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.0918	86	1147	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	76.9432	98	1147	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.7431	132	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:29,450] [INFO] DFAST Taxonomy check result was written to GCF_014646635.1_ASM1464663v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:29,451] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:29,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:29,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference/checkm_data
[2024-01-25 18:59:29,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:29,489] [INFO] Task started: CheckM
[2024-01-25 18:59:29,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646635.1_ASM1464663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646635.1_ASM1464663v1_genomic.fna/checkm_input GCF_014646635.1_ASM1464663v1_genomic.fna/checkm_result
[2024-01-25 18:59:56,236] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:56,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:56,252] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:56,252] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:56,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646635.1_ASM1464663v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:56,253] [INFO] Task started: Blastn
[2024-01-25 18:59:56,253] [INFO] Running command: blastn -query GCF_014646635.1_ASM1464663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga57523cd-ae8a-43ac-8617-2ca692ef3b1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646635.1_ASM1464663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:57,015] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:57,018] [INFO] Selected 14 target genomes.
[2024-01-25 18:59:57,018] [INFO] Target genome list was writen to GCF_014646635.1_ASM1464663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:57,035] [INFO] Task started: fastANI
[2024-01-25 18:59:57,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg158b9102-6a7f-4eac-8314-d943960efc79/GCF_014646635.1_ASM1464663v1_genomic.fna.gz --refList GCF_014646635.1_ASM1464663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646635.1_ASM1464663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:07,392] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:07,399] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:07,399] [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_014646635.1	s__Lentibacillus kapialis	100.0	1140	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000224785.1	s__Lentibacillus jeotgali	81.4668	694	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307805.1	s__Lentibacillus amyloliquefaciens	79.3515	446	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004565465.1	s__Lentibacillus salicampi	79.1822	487	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373365.1	s__Lentibacillus sp013373365	78.4857	433	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112045.1	s__Lentibacillus halodurans	78.2018	390	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112705.1	s__Lentibacillus persicus	77.794	298	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887555.1	s__Lentibacillus cibarius	77.2548	196	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.44	97.49	0.90	0.85	3	-
GCF_017873675.1	s__Lentibacillus litoralis	77.0992	130	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162695.1	s__Lentibacillus siamensis	76.9444	157	1147	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:07,401] [INFO] GTDB search result was written to GCF_014646635.1_ASM1464663v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:07,401] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:07,404] [INFO] DFAST_QC result json was written to GCF_014646635.1_ASM1464663v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:07,404] [INFO] DFAST_QC completed!
[2024-01-25 19:00:07,404] [INFO] Total running time: 0h1m2s