[2024-01-24 14:05:36,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference
[2024-01-24 14:05:37,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,387] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e2f7b99-a56a-4f72-8e27-cb97cedf3b90/GCF_004354545.1_ASM435454v1_genomic.fna.gz | prodigal -d GCF_004354545.1_ASM435454v1_genomic.fna/cds.fna -a GCF_004354545.1_ASM435454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:40,937] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:40,938] [INFO] Task started: HMMsearch
[2024-01-24 14:05:40,938] [INFO] Running command: hmmsearch --tblout GCF_004354545.1_ASM435454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference/reference_markers.hmm GCF_004354545.1_ASM435454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:41,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:41,177] [INFO] Found 6/6 markers.
[2024-01-24 14:05:41,198] [INFO] Query marker FASTA was written to GCF_004354545.1_ASM435454v1_genomic.fna/markers.fasta
[2024-01-24 14:05:41,198] [INFO] Task started: Blastn
[2024-01-24 14:05:41,198] [INFO] Running command: blastn -query GCF_004354545.1_ASM435454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference/reference_markers.fasta -out GCF_004354545.1_ASM435454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:41,785] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:41,790] [INFO] Selected 14 target genomes.
[2024-01-24 14:05:41,790] [INFO] Target genome list was writen to GCF_004354545.1_ASM435454v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:41,834] [INFO] Task started: fastANI
[2024-01-24 14:05:41,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e2f7b99-a56a-4f72-8e27-cb97cedf3b90/GCF_004354545.1_ASM435454v1_genomic.fna.gz --refList GCF_004354545.1_ASM435454v1_genomic.fna/target_genomes.txt --output GCF_004354545.1_ASM435454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:46,880] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:46,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:46,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:46,897] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:05:46,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:46,897] [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 amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	100.0	514	518	95	conclusive
Lactobacillus amylolyticus	strain=DSM 11664	GCA_000178475.1	83683	83683	type	True	99.9218	467	518	95	conclusive
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	99.9021	469	518	95	conclusive
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	81.1972	257	518	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	81.0488	236	518	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	81.0319	264	518	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	80.5242	228	518	95	below_threshold
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	80.5172	242	518	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	80.4743	219	518	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.1756	96	518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:46,899] [INFO] DFAST Taxonomy check result was written to GCF_004354545.1_ASM435454v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:46,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:46,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:46,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference/checkm_data
[2024-01-24 14:05:46,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:46,925] [INFO] Task started: CheckM
[2024-01-24 14:05:46,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354545.1_ASM435454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354545.1_ASM435454v1_genomic.fna/checkm_input GCF_004354545.1_ASM435454v1_genomic.fna/checkm_result
[2024-01-24 14:06:06,413] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:06,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,430] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:06,431] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:06,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354545.1_ASM435454v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:06,432] [INFO] Task started: Blastn
[2024-01-24 14:06:06,432] [INFO] Running command: blastn -query GCF_004354545.1_ASM435454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cf390e-41b1-4e83-b0e8-f103c85d2796/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354545.1_ASM435454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:07,265] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:07,268] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:07,269] [INFO] Target genome list was writen to GCF_004354545.1_ASM435454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:07,335] [INFO] Task started: fastANI
[2024-01-24 14:06:07,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e2f7b99-a56a-4f72-8e27-cb97cedf3b90/GCF_004354545.1_ASM435454v1_genomic.fna.gz --refList GCF_004354545.1_ASM435454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354545.1_ASM435454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:12,361] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:12,373] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:12,373] [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_000178475.1	s__Lactobacillus amylolyticus	99.9218	467	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	conclusive
GCF_002706375.1	s__Lactobacillus amylovorus	81.9639	249	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001434975.1	s__Lactobacillus gallinarum	81.406	232	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000615445.1	s__Lactobacillus hamsteri	81.1713	258	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000615285.1	s__Lactobacillus kitasatonis	81.0373	229	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_004009905.1	s__Lactobacillus xujianguonis	80.5417	241	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_001436305.1	s__Lactobacillus ultunensis	80.4674	220	518	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	80.4223	218	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	80.2708	221	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_000297025.1	s__Lactobacillus pasteurii	80.2437	174	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCF_001435325.1	s__Lactobacillus intestinalis	80.2199	207	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_001434335.1	s__Lactobacillus kalixensis	80.1178	231	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589675.1	s__Lactobacillus sp910589675	79.5009	131	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:12,376] [INFO] GTDB search result was written to GCF_004354545.1_ASM435454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:12,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:12,379] [INFO] DFAST_QC result json was written to GCF_004354545.1_ASM435454v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:12,384] [INFO] DFAST_QC completed!
[2024-01-24 14:06:12,385] [INFO] Total running time: 0h0m36s