[2024-01-24 13:55:18,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference
[2024-01-24 13:55:19,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:19,488] [INFO] Task started: Prodigal
[2024-01-24 13:55:19,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb67344e-9432-41ab-b12f-8382f1168fcc/GCF_014830205.1_ASM1483020v1_genomic.fna.gz | prodigal -d GCF_014830205.1_ASM1483020v1_genomic.fna/cds.fna -a GCF_014830205.1_ASM1483020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:23,859] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:23,860] [INFO] Task started: HMMsearch
[2024-01-24 13:55:23,860] [INFO] Running command: hmmsearch --tblout GCF_014830205.1_ASM1483020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference/reference_markers.hmm GCF_014830205.1_ASM1483020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:24,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:24,127] [INFO] Found 6/6 markers.
[2024-01-24 13:55:24,159] [INFO] Query marker FASTA was written to GCF_014830205.1_ASM1483020v1_genomic.fna/markers.fasta
[2024-01-24 13:55:24,160] [INFO] Task started: Blastn
[2024-01-24 13:55:24,161] [INFO] Running command: blastn -query GCF_014830205.1_ASM1483020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference/reference_markers.fasta -out GCF_014830205.1_ASM1483020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:24,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:24,754] [INFO] Selected 18 target genomes.
[2024-01-24 13:55:24,754] [INFO] Target genome list was writen to GCF_014830205.1_ASM1483020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:24,793] [INFO] Task started: fastANI
[2024-01-24 13:55:24,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb67344e-9432-41ab-b12f-8382f1168fcc/GCF_014830205.1_ASM1483020v1_genomic.fna.gz --refList GCF_014830205.1_ASM1483020v1_genomic.fna/target_genomes.txt --output GCF_014830205.1_ASM1483020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:31,959] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:31,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:31,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:31,969] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:55:31,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:55:31,970] [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 rudii	strain=STM3_1	GCA_014145455.1	2759755	2759755	type	True	83.702	483	713	95	below_threshold
Limosilactobacillus balticus	strain=BG-AF3-A	GCA_014145615.1	2759747	2759747	type	True	82.2739	420	713	95	below_threshold
Limosilactobacillus reuteri subsp. rodentium	strain=100-23	GCA_000168255.1	349123	1598	type	True	82.2587	431	713	95	below_threshold
Limosilactobacillus albertensis	strain=Lr3000	GCA_014145555.1	2759752	2759752	type	True	82.1579	455	713	95	below_threshold
Limosilactobacillus caviae	strain=CCM 8609	GCA_014635905.1	1769424	1769424	type	True	82.1092	455	713	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	82.0087	414	713	95	below_threshold
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	82.0052	394	713	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	81.9335	411	713	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	81.8814	388	713	95	below_threshold
Limosilactobacillus reuteri subsp. suis	strain=ATCC 53608	GCA_000236455.2	927703	1598	type	True	81.7196	408	713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:31,971] [INFO] DFAST Taxonomy check result was written to GCF_014830205.1_ASM1483020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:31,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:31,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:31,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference/checkm_data
[2024-01-24 13:55:31,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:32,002] [INFO] Task started: CheckM
[2024-01-24 13:55:32,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014830205.1_ASM1483020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014830205.1_ASM1483020v1_genomic.fna/checkm_input GCF_014830205.1_ASM1483020v1_genomic.fna/checkm_result
[2024-01-24 13:55:53,066] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:53,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:53,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:53,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:53,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014830205.1_ASM1483020v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:53,089] [INFO] Task started: Blastn
[2024-01-24 13:55:53,089] [INFO] Running command: blastn -query GCF_014830205.1_ASM1483020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7300d0-004d-4ce4-9ea8-e05b5c6ef2ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_014830205.1_ASM1483020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:53,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:53,932] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:53,932] [INFO] Target genome list was writen to GCF_014830205.1_ASM1483020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:53,942] [INFO] Task started: fastANI
[2024-01-24 13:55:53,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb67344e-9432-41ab-b12f-8382f1168fcc/GCF_014830205.1_ASM1483020v1_genomic.fna.gz --refList GCF_014830205.1_ASM1483020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014830205.1_ASM1483020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:59,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:59,141] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:59,141] [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_009663775.1	s__Limosilactobacillus sp009663775	98.5909	558	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.62	98.62	0.83	0.83	2	conclusive
GCF_014145455.1	s__Limosilactobacillus rudii	83.702	483	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014145615.1	s__Limosilactobacillus balticus	82.2594	419	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.51	98.51	0.89	0.89	2	-
GCF_014635905.1	s__Limosilactobacillus caviae	82.1174	456	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.34	95.38	0.89	0.84	7	-
GCF_000016825.1	s__Limosilactobacillus reuteri	81.9155	412	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCF_014145585.1	s__Limosilactobacillus agrestis	81.4478	380	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.60	98.25	0.88	0.88	3	-
GCA_003072625.1	s__Limosilactobacillus reuteri_D	81.3696	387	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	-
GCF_013694365.1	s__Limosilactobacillus reuteri_E	80.8509	359	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.28	96.40	0.80	0.72	58	-
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	79.1934	170	713	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:59,143] [INFO] GTDB search result was written to GCF_014830205.1_ASM1483020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:59,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:59,147] [INFO] DFAST_QC result json was written to GCF_014830205.1_ASM1483020v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:59,147] [INFO] DFAST_QC completed!
[2024-01-24 13:55:59,147] [INFO] Total running time: 0h0m41s