[2024-01-24 14:05:53,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference
[2024-01-24 14:05:54,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:54,934] [INFO] Task started: Prodigal
[2024-01-24 14:05:54,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg99edaabf-8ffe-47c8-a1c3-18e4036bbd6c/GCF_012641075.1_ASM1264107v1_genomic.fna.gz | prodigal -d GCF_012641075.1_ASM1264107v1_genomic.fna/cds.fna -a GCF_012641075.1_ASM1264107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:01,029] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:01,029] [INFO] Task started: HMMsearch
[2024-01-24 14:06:01,029] [INFO] Running command: hmmsearch --tblout GCF_012641075.1_ASM1264107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference/reference_markers.hmm GCF_012641075.1_ASM1264107v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:01,308] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:01,309] [INFO] Found 6/6 markers.
[2024-01-24 14:06:01,343] [INFO] Query marker FASTA was written to GCF_012641075.1_ASM1264107v1_genomic.fna/markers.fasta
[2024-01-24 14:06:01,343] [INFO] Task started: Blastn
[2024-01-24 14:06:01,343] [INFO] Running command: blastn -query GCF_012641075.1_ASM1264107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference/reference_markers.fasta -out GCF_012641075.1_ASM1264107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:01,996] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:02,000] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:02,001] [INFO] Target genome list was writen to GCF_012641075.1_ASM1264107v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:02,080] [INFO] Task started: fastANI
[2024-01-24 14:06:02,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg99edaabf-8ffe-47c8-a1c3-18e4036bbd6c/GCF_012641075.1_ASM1264107v1_genomic.fna.gz --refList GCF_012641075.1_ASM1264107v1_genomic.fna/target_genomes.txt --output GCF_012641075.1_ASM1264107v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:11,301] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:11,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:11,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:11,312] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:11,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:11,313] [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
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	100.0	832	833	95	conclusive
Secundilactobacillus yichangensis	strain=F79-211-2	GCA_016861565.1	2799580	2799580	type	True	84.0687	556	833	95	below_threshold
Secundilactobacillus silagincola	strain=IWT5	GCA_002583405.1	1714681	1714681	type	True	82.9599	504	833	95	below_threshold
Secundilactobacillus mixtipabuli	strain=IWT30	GCA_002217925.1	1435342	1435342	type	True	82.509	502	833	95	below_threshold
Secundilactobacillus pentosiphilus	strain=IWT25	GCA_002217985.1	1714682	1714682	type	True	82.378	482	833	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	81.4093	456	833	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	81.3773	453	833	95	below_threshold
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	81.3373	453	833	95	below_threshold
Secundilactobacillus similis	strain=JCM 2765	GCA_001311075.1	414682	414682	type	True	79.8077	201	833	95	below_threshold
Levilactobacillus huananensis	strain=151-2B	GCA_003946145.1	2486019	2486019	type	True	79.2439	69	833	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	77.4303	64	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:11,315] [INFO] DFAST Taxonomy check result was written to GCF_012641075.1_ASM1264107v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:11,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:11,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:11,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference/checkm_data
[2024-01-24 14:06:11,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:11,346] [INFO] Task started: CheckM
[2024-01-24 14:06:11,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012641075.1_ASM1264107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012641075.1_ASM1264107v1_genomic.fna/checkm_input GCF_012641075.1_ASM1264107v1_genomic.fna/checkm_result
[2024-01-24 14:06:37,674] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:37,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:37,694] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:37,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:37,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012641075.1_ASM1264107v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:37,695] [INFO] Task started: Blastn
[2024-01-24 14:06:37,695] [INFO] Running command: blastn -query GCF_012641075.1_ASM1264107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bf6a647-3228-476d-b88e-c05b7f4b11b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012641075.1_ASM1264107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:38,519] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:38,522] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:38,523] [INFO] Target genome list was writen to GCF_012641075.1_ASM1264107v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:38,529] [INFO] Task started: fastANI
[2024-01-24 14:06:38,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg99edaabf-8ffe-47c8-a1c3-18e4036bbd6c/GCF_012641075.1_ASM1264107v1_genomic.fna.gz --refList GCF_012641075.1_ASM1264107v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012641075.1_ASM1264107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:45,232] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:45,240] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:45,240] [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_012641075.1	s__Secundilactobacillus sp012641075	100.0	832	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016861565.1	s__Secundilactobacillus sp016861565	84.0687	556	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583405.1	s__Secundilactobacillus silagincola	82.9585	505	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	82.5209	501	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217985.1	s__Secundilactobacillus pentosiphilus	82.3615	483	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.11	97.11	0.89	0.89	2	-
GCF_002217945.1	s__Secundilactobacillus silagei	81.4093	456	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	-
GCF_005405185.1	s__Secundilactobacillus sp005405185	81.3373	453	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311075.1	s__Secundilactobacillus similis	79.81	200	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.93	99.93	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:45,242] [INFO] GTDB search result was written to GCF_012641075.1_ASM1264107v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:45,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:45,245] [INFO] DFAST_QC result json was written to GCF_012641075.1_ASM1264107v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:45,245] [INFO] DFAST_QC completed!
[2024-01-24 14:06:45,245] [INFO] Total running time: 0h0m52s