[2024-01-24 10:57:05,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:05,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:05,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference
[2024-01-24 10:57:06,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:06,931] [INFO] Task started: Prodigal
[2024-01-24 10:57:06,931] [INFO] Running command: gunzip -c /var/lib/cwl/stgb71b4e62-4131-4ffd-bfda-afe2eb91c33b/GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna.gz | prodigal -d GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/cds.fna -a GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:10,335] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:10,335] [INFO] Task started: HMMsearch
[2024-01-24 10:57:10,336] [INFO] Running command: hmmsearch --tblout GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference/reference_markers.hmm GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:10,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:10,580] [INFO] Found 6/6 markers.
[2024-01-24 10:57:10,603] [INFO] Query marker FASTA was written to GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/markers.fasta
[2024-01-24 10:57:10,604] [INFO] Task started: Blastn
[2024-01-24 10:57:10,604] [INFO] Running command: blastn -query GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference/reference_markers.fasta -out GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:11,190] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:11,194] [INFO] Selected 20 target genomes.
[2024-01-24 10:57:11,194] [INFO] Target genome list was writen to GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/target_genomes.txt
[2024-01-24 10:57:11,242] [INFO] Task started: fastANI
[2024-01-24 10:57:11,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgb71b4e62-4131-4ffd-bfda-afe2eb91c33b/GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna.gz --refList GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/target_genomes.txt --output GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:17,546] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:17,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:17,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:17,623] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:17,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:17,623] [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
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	81.3805	312	599	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	81.3771	313	599	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	80.2959	168	599	95	below_threshold
Lactobacillus kalixensis	strain=DSM 16043	GCA_001434335.1	227944	227944	type	True	80.1882	241	599	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_001435325.1	151781	151781	type	True	80.1446	253	599	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.1005	262	599	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	80.0929	199	599	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	80.0724	248	599	95	below_threshold
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	80.0571	254	599	95	below_threshold
Lactobacillus acidophilus	strain=CIP 76.13	GCA_000469705.1	1579	1579	type	True	80.0092	254	599	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	79.9268	260	599	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	79.7717	227	599	95	below_threshold
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	79.5819	228	599	95	below_threshold
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	79.5161	236	599	95	below_threshold
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	79.5007	226	599	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	79.4346	222	599	95	below_threshold
Lactobacillus apis	strain=CCM 8403	GCA_014635365.1	303541	303541	type	True	78.32	128	599	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.2922	110	599	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	77.843	102	599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:17,625] [INFO] DFAST Taxonomy check result was written to GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/tc_result.tsv
[2024-01-24 10:57:17,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:17,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:17,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference/checkm_data
[2024-01-24 10:57:17,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:17,652] [INFO] Task started: CheckM
[2024-01-24 10:57:17,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/checkm_input GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/checkm_result
[2024-01-24 10:57:37,241] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:37,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:37,263] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:37,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:37,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/markers.fasta)
[2024-01-24 10:57:37,265] [INFO] Task started: Blastn
[2024-01-24 10:57:37,265] [INFO] Running command: blastn -query GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c510ff7-8d8b-4dec-8fe2-170f5390955b/dqc_reference/reference_markers_gtdb.fasta -out GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:38,166] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:38,171] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:38,171] [INFO] Target genome list was writen to GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:38,182] [INFO] Task started: fastANI
[2024-01-24 10:57:38,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgb71b4e62-4131-4ffd-bfda-afe2eb91c33b/GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna.gz --refList GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/target_genomes_gtdb.txt --output GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:57:43,454] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:43,501] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:57:43,501] [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
GCA_014803915.1	s__Lactobacillus sp014803915	98.3714	342	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000615445.1	s__Lactobacillus hamsteri	81.3889	311	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001434335.1	s__Lactobacillus kalixensis	80.1649	242	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435325.1	s__Lactobacillus intestinalis	80.1446	253	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_004009905.1	s__Lactobacillus xujianguonis	80.0273	255	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_001591845.1	s__Lactobacillus acidophilus	80.0039	253	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000178475.1	s__Lactobacillus amylolyticus	79.9849	200	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_000160855.1	s__Lactobacillus helveticus	79.9427	236	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_007570935.1	s__Lactobacillus sp007570935	79.8948	236	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436305.1	s__Lactobacillus ultunensis	79.7717	227	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCA_018883635.1	s__Lactobacillus pullistercoris	79.6332	228	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018987235.1	s__Lactobacillus crispatus	79.5159	236	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_002837055.1	s__Lactobacillus apis	78.2922	110	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.63	96.48	0.93	0.86	10	-
--------------------------------------------------------------------------------
[2024-01-24 10:57:43,504] [INFO] GTDB search result was written to GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/result_gtdb.tsv
[2024-01-24 10:57:43,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:57:43,511] [INFO] DFAST_QC result json was written to GCF_943193025.1_Lactobacillus_sp_nov_DSM110155_genomic.fna/dqc_result.json
[2024-01-24 10:57:43,512] [INFO] DFAST_QC completed!
[2024-01-24 10:57:43,512] [INFO] Total running time: 0h0m38s