[2024-01-24 13:40:55,391] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference
[2024-01-24 13:40:56,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,675] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8ac2f2e-85f8-4b10-a58e-1adf3958a96c/GCF_014145455.1_ASM1414545v1_genomic.fna.gz | prodigal -d GCF_014145455.1_ASM1414545v1_genomic.fna/cds.fna -a GCF_014145455.1_ASM1414545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,687] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,687] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,687] [INFO] Running command: hmmsearch --tblout GCF_014145455.1_ASM1414545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference/reference_markers.hmm GCF_014145455.1_ASM1414545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,930] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,958] [INFO] Query marker FASTA was written to GCF_014145455.1_ASM1414545v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,958] [INFO] Task started: Blastn
[2024-01-24 13:41:00,958] [INFO] Running command: blastn -query GCF_014145455.1_ASM1414545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference/reference_markers.fasta -out GCF_014145455.1_ASM1414545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,528] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,531] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:01,532] [INFO] Target genome list was writen to GCF_014145455.1_ASM1414545v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,548] [INFO] Task started: fastANI
[2024-01-24 13:41:01,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8ac2f2e-85f8-4b10-a58e-1adf3958a96c/GCF_014145455.1_ASM1414545v1_genomic.fna.gz --refList GCF_014145455.1_ASM1414545v1_genomic.fna/target_genomes.txt --output GCF_014145455.1_ASM1414545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:10,042] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:10,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:10,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:10,052] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:10,052] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:10,052] [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	100.0	753	754	95	conclusive
Limosilactobacillus caviae	strain=CCM 8609	GCA_014635905.1	1769424	1769424	type	True	81.9436	450	754	95	below_threshold
Limosilactobacillus albertensis	strain=Lr3000	GCA_014145555.1	2759752	2759752	type	True	81.783	435	754	95	below_threshold
Limosilactobacillus balticus	strain=BG-AF3-A	GCA_014145615.1	2759747	2759747	type	True	81.543	425	754	95	below_threshold
Limosilactobacillus reuteri subsp. suis	strain=ATCC 53608	GCA_000236455.2	927703	1598	type	True	81.4567	380	754	95	below_threshold
Limosilactobacillus reuteri subsp. rodentium	strain=100-23	GCA_000168255.1	349123	1598	type	True	81.2713	403	754	95	below_threshold
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	81.226	384	754	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	81.1594	393	754	95	below_threshold
Limosilactobacillus agrestis	strain=WF-MT5-A	GCA_014145585.1	2759748	2759748	type	True	81.0268	363	754	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	80.9974	372	754	95	below_threshold
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	79.5581	159	754	95	below_threshold
Limosilactobacillus fastidiosus	strain=WF-MO7-1	GCA_014145505.1	2759855	2759855	type	True	79.4044	174	754	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	78.983	118	754	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	78.7822	122	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,054] [INFO] DFAST Taxonomy check result was written to GCF_014145455.1_ASM1414545v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:10,054] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:10,054] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:10,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference/checkm_data
[2024-01-24 13:41:10,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:10,080] [INFO] Task started: CheckM
[2024-01-24 13:41:10,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145455.1_ASM1414545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145455.1_ASM1414545v1_genomic.fna/checkm_input GCF_014145455.1_ASM1414545v1_genomic.fna/checkm_result
[2024-01-24 13:41:27,749] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:27,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,767] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:27,767] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:27,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145455.1_ASM1414545v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:27,767] [INFO] Task started: Blastn
[2024-01-24 13:41:27,767] [INFO] Running command: blastn -query GCF_014145455.1_ASM1414545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc33b41c6-abfc-45cf-870c-0cf0b318841e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145455.1_ASM1414545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:28,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:28,484] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:28,484] [INFO] Target genome list was writen to GCF_014145455.1_ASM1414545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:28,489] [INFO] Task started: fastANI
[2024-01-24 13:41:28,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8ac2f2e-85f8-4b10-a58e-1adf3958a96c/GCF_014145455.1_ASM1414545v1_genomic.fna.gz --refList GCF_014145455.1_ASM1414545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145455.1_ASM1414545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:33,338] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,346] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:33,346] [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_014145455.1	s__Limosilactobacillus rudii	100.0	753	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009663775.1	s__Limosilactobacillus sp009663775	83.5702	466	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.62	98.62	0.83	0.83	2	-
GCF_014635905.1	s__Limosilactobacillus caviae	81.9315	450	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.34	95.38	0.89	0.84	7	-
GCF_014145615.1	s__Limosilactobacillus balticus	81.5319	426	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.51	98.51	0.89	0.89	2	-
GCF_000016825.1	s__Limosilactobacillus reuteri	81.0751	400	754	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	81.0268	363	754	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	81.017	379	754	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	80.712	340	754	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	79.5591	159	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCF_014145505.1	s__Limosilactobacillus fastidiosus	79.3927	175	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.58	99.58	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,347] [INFO] GTDB search result was written to GCF_014145455.1_ASM1414545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:33,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:33,351] [INFO] DFAST_QC result json was written to GCF_014145455.1_ASM1414545v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:33,351] [INFO] DFAST_QC completed!
[2024-01-24 13:41:33,351] [INFO] Total running time: 0h0m38s