[2024-01-24 15:06:36,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:37,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:37,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference
[2024-01-24 15:06:38,370] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,371] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,371] [INFO] Running command: gunzip -c /var/lib/cwl/stga295ed45-c220-4998-b61b-dc0329d81401/GCF_016587775.1_ASM1658777v1_genomic.fna.gz | prodigal -d GCF_016587775.1_ASM1658777v1_genomic.fna/cds.fna -a GCF_016587775.1_ASM1658777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:43,916] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:43,916] [INFO] Task started: HMMsearch
[2024-01-24 15:06:43,917] [INFO] Running command: hmmsearch --tblout GCF_016587775.1_ASM1658777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference/reference_markers.hmm GCF_016587775.1_ASM1658777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:44,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:44,197] [INFO] Found 6/6 markers.
[2024-01-24 15:06:44,221] [INFO] Query marker FASTA was written to GCF_016587775.1_ASM1658777v1_genomic.fna/markers.fasta
[2024-01-24 15:06:44,221] [INFO] Task started: Blastn
[2024-01-24 15:06:44,221] [INFO] Running command: blastn -query GCF_016587775.1_ASM1658777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference/reference_markers.fasta -out GCF_016587775.1_ASM1658777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:44,926] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:44,930] [INFO] Selected 16 target genomes.
[2024-01-24 15:06:44,930] [INFO] Target genome list was writen to GCF_016587775.1_ASM1658777v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:44,949] [INFO] Task started: fastANI
[2024-01-24 15:06:44,950] [INFO] Running command: fastANI --query /var/lib/cwl/stga295ed45-c220-4998-b61b-dc0329d81401/GCF_016587775.1_ASM1658777v1_genomic.fna.gz --refList GCF_016587775.1_ASM1658777v1_genomic.fna/target_genomes.txt --output GCF_016587775.1_ASM1658777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:06:52,280] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:52,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:06:52,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:06:52,292] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:06:52,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:06:52,293] [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 nasalidis	strain=YZ01	GCA_016587775.1	2797258	2797258	type	True	100.0	500	509	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_001888925.1	1537158	1584	suspected-type	True	87.1891	345	509	95	below_threshold
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_000192165.1	29397	1584	suspected-type	True	87.1879	360	509	95	below_threshold
Lactobacillus delbrueckii subsp. delbrueckii	strain=NBRC 3202	GCA_006740305.1	83684	1584	suspected-type	True	87.1648	352	509	95	below_threshold
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001888965.1	1050107	1584	suspected-type	True	87.1639	367	509	95	below_threshold
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001190005.1	1050107	1584	suspected-type	True	87.0779	366	509	95	below_threshold
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001433875.1	83684	1584	suspected-type	True	87.0736	320	509	95	below_threshold
Lactobacillus delbrueckii subsp. bulgaricus	strain=NBRC 13953	GCA_006539405.1	1585	1584	type	True	87.0658	322	509	95	below_threshold
Lactobacillus delbrueckii subsp. indicus	strain=JCM 15610	GCA_001189855.1	249265	1584	type	True	86.8826	347	509	95	below_threshold
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_002278095.1	29397	1584	type	True	86.8776	375	509	95	below_threshold
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001908495.1	83684	1584	type	True	86.8269	347	509	95	below_threshold
Lactobacillus delbrueckii subsp. bulgaricus	strain=DSM 20081	GCA_001437195.1	1585	1584	type	True	86.7619	333	509	95	below_threshold
Lactobacillus delbrueckii subsp. bulgaricus	strain=ATCC 11842	GCA_000056065.1	1585	1584	type	True	86.7049	348	509	95	below_threshold
Lactobacillus delbrueckii subsp. indicus	strain=DSM 15996	GCA_001435795.1	249265	1584	type	True	86.6822	349	509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:06:52,294] [INFO] DFAST Taxonomy check result was written to GCF_016587775.1_ASM1658777v1_genomic.fna/tc_result.tsv
[2024-01-24 15:06:52,295] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:06:52,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:06:52,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference/checkm_data
[2024-01-24 15:06:52,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:06:52,320] [INFO] Task started: CheckM
[2024-01-24 15:06:52,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016587775.1_ASM1658777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016587775.1_ASM1658777v1_genomic.fna/checkm_input GCF_016587775.1_ASM1658777v1_genomic.fna/checkm_result
[2024-01-24 15:07:15,584] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:15,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:15,609] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:15,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:15,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016587775.1_ASM1658777v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:15,610] [INFO] Task started: Blastn
[2024-01-24 15:07:15,610] [INFO] Running command: blastn -query GCF_016587775.1_ASM1658777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d4100be-fffd-4a09-b350-1fa52260de45/dqc_reference/reference_markers_gtdb.fasta -out GCF_016587775.1_ASM1658777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:16,542] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:16,545] [INFO] Selected 9 target genomes.
[2024-01-24 15:07:16,545] [INFO] Target genome list was writen to GCF_016587775.1_ASM1658777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:16,553] [INFO] Task started: fastANI
[2024-01-24 15:07:16,554] [INFO] Running command: fastANI --query /var/lib/cwl/stga295ed45-c220-4998-b61b-dc0329d81401/GCF_016587775.1_ASM1658777v1_genomic.fna.gz --refList GCF_016587775.1_ASM1658777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016587775.1_ASM1658777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:20,257] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:20,264] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:07:20,264] [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_016587775.1	s__Lactobacillus nasalidis	100.0	500	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.92	99.91	0.92	0.89	3	conclusive
GCF_001433875.1	s__Lactobacillus delbrueckii	87.0827	320	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.56	96.59	0.89	0.81	103	-
GCA_004556255.1	s__Lactobacillus delbrueckii_B	86.7879	263	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695985.1	s__Lactobacillus porci	82.4846	312	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.20	0.91	0.90	4	-
GCF_001434815.1	s__Lactobacillus equicursoris	81.5648	287	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.84	97.67	0.88	0.82	5	-
GCA_905214545.1	s__Lactobacillus sp905214545	78.1651	88	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:07:20,265] [INFO] GTDB search result was written to GCF_016587775.1_ASM1658777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:20,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:20,270] [INFO] DFAST_QC result json was written to GCF_016587775.1_ASM1658777v1_genomic.fna/dqc_result.json
[2024-01-24 15:07:20,270] [INFO] DFAST_QC completed!
[2024-01-24 15:07:20,270] [INFO] Total running time: 0h0m43s