[2024-01-24 13:57:45,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:45,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:45,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference
[2024-01-24 13:57:46,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,641] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgc629c176-2fcd-45e5-8cc6-e1459dc29a87/GCF_005887555.1_ASM588755v1_genomic.fna.gz | prodigal -d GCF_005887555.1_ASM588755v1_genomic.fna/cds.fna -a GCF_005887555.1_ASM588755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,094] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,095] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,095] [INFO] Running command: hmmsearch --tblout GCF_005887555.1_ASM588755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference/reference_markers.hmm GCF_005887555.1_ASM588755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,383] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,423] [INFO] Query marker FASTA was written to GCF_005887555.1_ASM588755v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,424] [INFO] Task started: Blastn
[2024-01-24 13:57:56,424] [INFO] Running command: blastn -query GCF_005887555.1_ASM588755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference/reference_markers.fasta -out GCF_005887555.1_ASM588755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,038] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:57,039] [INFO] Target genome list was writen to GCF_005887555.1_ASM588755v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,050] [INFO] Task started: fastANI
[2024-01-24 13:57:57,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgc629c176-2fcd-45e5-8cc6-e1459dc29a87/GCF_005887555.1_ASM588755v1_genomic.fna.gz --refList GCF_005887555.1_ASM588755v1_genomic.fna/target_genomes.txt --output GCF_005887555.1_ASM588755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:11,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:11,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:11,946] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:11,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:11,946] [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 cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	100.0	1214	1218	95	conclusive
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	78.7466	227	1218	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	78.6604	221	1218	95	below_threshold
Virgibacillus ihumii	strain=Marseille-Q1233	GCA_902726655.1	2686091	2686091	type	True	78.5294	143	1218	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	77.5977	184	1218	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.5242	70	1218	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.4886	73	1218	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	77.3526	254	1218	95	below_threshold
Lentibacillus persicus	strain=DSM 22530	GCA_900112705.1	640948	640948	type	True	77.3329	169	1218	95	below_threshold
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	77.3146	182	1218	95	below_threshold
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	77.1498	79	1218	95	below_threshold
Lentibacillus sediminis	strain=0W14	GCA_002763455.1	1940529	1940529	type	True	76.7763	84	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,948] [INFO] DFAST Taxonomy check result was written to GCF_005887555.1_ASM588755v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:11,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:11,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:11,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference/checkm_data
[2024-01-24 13:58:11,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:11,991] [INFO] Task started: CheckM
[2024-01-24 13:58:11,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005887555.1_ASM588755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005887555.1_ASM588755v1_genomic.fna/checkm_input GCF_005887555.1_ASM588755v1_genomic.fna/checkm_result
[2024-01-24 13:58:47,001] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:47,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:47,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:47,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005887555.1_ASM588755v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:47,024] [INFO] Task started: Blastn
[2024-01-24 13:58:47,024] [INFO] Running command: blastn -query GCF_005887555.1_ASM588755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815b79dd-942b-499d-a5c9-2965ec32f381/dqc_reference/reference_markers_gtdb.fasta -out GCF_005887555.1_ASM588755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:47,790] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:47,795] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:47,795] [INFO] Target genome list was writen to GCF_005887555.1_ASM588755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:47,813] [INFO] Task started: fastANI
[2024-01-24 13:58:47,813] [INFO] Running command: fastANI --query /var/lib/cwl/stgc629c176-2fcd-45e5-8cc6-e1459dc29a87/GCF_005887555.1_ASM588755v1_genomic.fna.gz --refList GCF_005887555.1_ASM588755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005887555.1_ASM588755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:01,790] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:01,805] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:01,806] [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_005887555.1	s__Lentibacillus cibarius	100.0	1214	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.44	97.49	0.90	0.85	3	conclusive
GCA_004145795.1	s__Lentibacillus lipolyticus	81.2814	538	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001311805.1	s__Lentibacillus juripiscarius	79.6693	483	1218	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_000224785.1	s__Lentibacillus jeotgali	78.8108	228	1218	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	78.6191	222	1218	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_900258515.1	s__Virgibacillus_E sp900258515	77.6644	117	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806455.1	s__Lentibacillus doumboii	77.5882	185	1218	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_014905415.1	s__Virgibacillus salexigens	77.4752	76	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_900112045.1	s__Lentibacillus halodurans	77.341	255	1218	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_014646635.1	s__Lentibacillus kapialis	77.293	181	1218	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_000709085.1	s__Virgibacillus_B alimentarius	77.1498	79	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_B	95.0	99.59	99.59	0.92	0.92	2	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	76.9745	59	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002763455.1	s__Lentibacillus_A sediminis	76.7489	85	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821065.1	s__Oceanobacillus oncorhynchi	76.379	72	1218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.79	98.49	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:01,807] [INFO] GTDB search result was written to GCF_005887555.1_ASM588755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:01,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:01,812] [INFO] DFAST_QC result json was written to GCF_005887555.1_ASM588755v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:01,812] [INFO] DFAST_QC completed!
[2024-01-24 13:59:01,812] [INFO] Total running time: 0h1m17s