[2024-01-24 13:46:10,811] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference
[2024-01-24 13:46:12,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,102] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg89f2702d-19cf-4229-8102-8196ebd91f71/GCF_014640495.1_ASM1464049v1_genomic.fna.gz | prodigal -d GCF_014640495.1_ASM1464049v1_genomic.fna/cds.fna -a GCF_014640495.1_ASM1464049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:20,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:20,144] [INFO] Task started: HMMsearch
[2024-01-24 13:46:20,144] [INFO] Running command: hmmsearch --tblout GCF_014640495.1_ASM1464049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference/reference_markers.hmm GCF_014640495.1_ASM1464049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:20,450] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:20,452] [INFO] Found 6/6 markers.
[2024-01-24 13:46:20,492] [INFO] Query marker FASTA was written to GCF_014640495.1_ASM1464049v1_genomic.fna/markers.fasta
[2024-01-24 13:46:20,492] [INFO] Task started: Blastn
[2024-01-24 13:46:20,493] [INFO] Running command: blastn -query GCF_014640495.1_ASM1464049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference/reference_markers.fasta -out GCF_014640495.1_ASM1464049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:21,191] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:21,194] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:21,195] [INFO] Target genome list was writen to GCF_014640495.1_ASM1464049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:21,206] [INFO] Task started: fastANI
[2024-01-24 13:46:21,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f2702d-19cf-4229-8102-8196ebd91f71/GCF_014640495.1_ASM1464049v1_genomic.fna.gz --refList GCF_014640495.1_ASM1464049v1_genomic.fna/target_genomes.txt --output GCF_014640495.1_ASM1464049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:33,087] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:33,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:33,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:33,105] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:33,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:33,105] [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
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	100.0	1453	1453	95	conclusive
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	99.9967	1448	1453	95	conclusive
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	81.6064	762	1453	95	below_threshold
Gottfriedia acidiceleris	strain=NRRL B-41736	GCA_002156925.1	371036	371036	type	True	81.3572	744	1453	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	81.355	737	1453	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	78.9304	364	1453	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	77.0856	134	1453	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	77.0663	147	1453	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.0415	87	1453	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.9238	144	1453	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	76.5868	103	1453	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	76.3365	57	1453	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:33,106] [INFO] DFAST Taxonomy check result was written to GCF_014640495.1_ASM1464049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:33,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:33,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:33,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference/checkm_data
[2024-01-24 13:46:33,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:33,151] [INFO] Task started: CheckM
[2024-01-24 13:46:33,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640495.1_ASM1464049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640495.1_ASM1464049v1_genomic.fna/checkm_input GCF_014640495.1_ASM1464049v1_genomic.fna/checkm_result
[2024-01-24 13:47:06,717] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:06,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,740] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:06,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:06,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640495.1_ASM1464049v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:06,741] [INFO] Task started: Blastn
[2024-01-24 13:47:06,741] [INFO] Running command: blastn -query GCF_014640495.1_ASM1464049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dc4c267-9d21-4c20-aff4-5f275a70398b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640495.1_ASM1464049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:07,534] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:07,537] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:07,537] [INFO] Target genome list was writen to GCF_014640495.1_ASM1464049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:07,556] [INFO] Task started: fastANI
[2024-01-24 13:47:07,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f2702d-19cf-4229-8102-8196ebd91f71/GCF_014640495.1_ASM1464049v1_genomic.fna.gz --refList GCF_014640495.1_ASM1464049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640495.1_ASM1464049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:20,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:20,300] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:20,300] [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_002128405.1	s__Gottfriedia solisilvae	99.9967	1448	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	conclusive
GCF_003053645.1	s__Gottfriedia sp003053645	86.243	1107	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156875.1	s__Gottfriedia sp002156875	82.25	894	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002559405.1	s__Gottfriedia sp002559405	81.6378	662	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156865.1	s__Gottfriedia luciferensis	81.5877	764	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420605.1	s__Gottfriedia sp001420605	81.4849	739	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564465.1	s__Gottfriedia sp002564465	81.4058	757	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.47	95.21	0.86	0.86	4	-
GCF_002577195.1	s__Gottfriedia sp002577195	81.3867	743	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712755.1	s__Gottfriedia luciferensis_B	81.3188	755	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
GCF_002574545.1	s__Gottfriedia sp002574545	81.2147	700	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013200995.1	s__Gottfriedia sp002556365	81.0434	737	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.58	95.58	0.84	0.83	3	-
GCF_004340305.1	s__Gottfriedia sp004340305	80.3459	658	1453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:20,302] [INFO] GTDB search result was written to GCF_014640495.1_ASM1464049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:20,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:20,311] [INFO] DFAST_QC result json was written to GCF_014640495.1_ASM1464049v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:20,311] [INFO] DFAST_QC completed!
[2024-01-24 13:47:20,311] [INFO] Total running time: 0h1m9s