[2024-01-24 11:26:54,314] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference
[2024-01-24 11:26:58,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg831e1488-6b86-4fac-9bf0-4c60a3a1d19e/GCF_014635905.1_ASM1463590v1_genomic.fna.gz | prodigal -d GCF_014635905.1_ASM1463590v1_genomic.fna/cds.fna -a GCF_014635905.1_ASM1463590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:02,874] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:02,874] [INFO] Task started: HMMsearch
[2024-01-24 11:27:02,875] [INFO] Running command: hmmsearch --tblout GCF_014635905.1_ASM1463590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference/reference_markers.hmm GCF_014635905.1_ASM1463590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:03,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:03,112] [INFO] Found 6/6 markers.
[2024-01-24 11:27:03,139] [INFO] Query marker FASTA was written to GCF_014635905.1_ASM1463590v1_genomic.fna/markers.fasta
[2024-01-24 11:27:03,139] [INFO] Task started: Blastn
[2024-01-24 11:27:03,139] [INFO] Running command: blastn -query GCF_014635905.1_ASM1463590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference/reference_markers.fasta -out GCF_014635905.1_ASM1463590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:03,722] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:03,725] [INFO] Selected 14 target genomes.
[2024-01-24 11:27:03,725] [INFO] Target genome list was writen to GCF_014635905.1_ASM1463590v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:03,781] [INFO] Task started: fastANI
[2024-01-24 11:27:03,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg831e1488-6b86-4fac-9bf0-4c60a3a1d19e/GCF_014635905.1_ASM1463590v1_genomic.fna.gz --refList GCF_014635905.1_ASM1463590v1_genomic.fna/target_genomes.txt --output GCF_014635905.1_ASM1463590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:09,847] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:09,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:09,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:09,857] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:09,857] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:09,857] [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
Limosilactobacillus caviae	strain=CCM 8609	GCA_014635905.1	1769424	1769424	type	True	100.0	758	758	95	inconclusive
Limosilactobacillus albertensis	strain=Lr3000	GCA_014145555.1	2759752	2759752	type	True	95.3588	655	758	95	inconclusive
Limosilactobacillus balticus	strain=BG-AF3-A	GCA_014145615.1	2759747	2759747	type	True	83.65	486	758	95	below_threshold
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	83.3546	431	758	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	83.1339	437	758	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	83.1133	450	758	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	83.0945	462	758	95	below_threshold
Limosilactobacillus reuteri subsp. rodentium	strain=100-23	GCA_000168255.1	349123	1598	type	True	83.085	496	758	95	below_threshold
Limosilactobacillus rudii	strain=STM3_1	GCA_014145455.1	2759755	2759755	type	True	81.9217	453	758	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=JCM 18461	GCA_001311505.1	1193095	1193095	type	True	77.5466	51	758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:09,859] [INFO] DFAST Taxonomy check result was written to GCF_014635905.1_ASM1463590v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:09,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:09,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:09,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference/checkm_data
[2024-01-24 11:27:09,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:09,889] [INFO] Task started: CheckM
[2024-01-24 11:27:09,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635905.1_ASM1463590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635905.1_ASM1463590v1_genomic.fna/checkm_input GCF_014635905.1_ASM1463590v1_genomic.fna/checkm_result
[2024-01-24 11:27:30,854] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:30,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,874] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:30,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:30,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635905.1_ASM1463590v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:30,875] [INFO] Task started: Blastn
[2024-01-24 11:27:30,875] [INFO] Running command: blastn -query GCF_014635905.1_ASM1463590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56a0d07a-6a4d-440b-bb76-f7340e4cca75/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635905.1_ASM1463590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:31,673] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:31,677] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:31,677] [INFO] Target genome list was writen to GCF_014635905.1_ASM1463590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:31,690] [INFO] Task started: fastANI
[2024-01-24 11:27:31,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg831e1488-6b86-4fac-9bf0-4c60a3a1d19e/GCF_014635905.1_ASM1463590v1_genomic.fna.gz --refList GCF_014635905.1_ASM1463590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635905.1_ASM1463590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:35,625] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:35,632] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:35,633] [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_014635905.1	s__Limosilactobacillus caviae	100.0	758	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.34	95.38	0.89	0.84	7	conclusive
GCF_014145615.1	s__Limosilactobacillus balticus	83.65	486	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.51	98.51	0.89	0.89	2	-
GCF_013694365.1	s__Limosilactobacillus reuteri_E	83.1754	423	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.28	96.40	0.80	0.72	58	-
GCF_000016825.1	s__Limosilactobacillus reuteri	83.1033	451	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCA_003072625.1	s__Limosilactobacillus reuteri_D	82.8828	427	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	-
GCF_014145585.1	s__Limosilactobacillus agrestis	82.8251	425	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.60	98.25	0.88	0.88	3	-
GCF_009663775.1	s__Limosilactobacillus sp009663775	82.4398	442	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.62	98.62	0.83	0.83	2	-
GCF_014145455.1	s__Limosilactobacillus rudii	81.9293	452	758	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,634] [INFO] GTDB search result was written to GCF_014635905.1_ASM1463590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:35,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:35,638] [INFO] DFAST_QC result json was written to GCF_014635905.1_ASM1463590v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:35,638] [INFO] DFAST_QC completed!
[2024-01-24 11:27:35,639] [INFO] Total running time: 0h0m41s