[2024-01-24 13:19:26,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference
[2024-01-24 13:19:27,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,826] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg757edc6c-ff1e-42cf-9e65-8dcd62dd8ca3/GCF_007095465.1_ASM709546v1_genomic.fna.gz | prodigal -d GCF_007095465.1_ASM709546v1_genomic.fna/cds.fna -a GCF_007095465.1_ASM709546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:30,791] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:30,791] [INFO] Task started: HMMsearch
[2024-01-24 13:19:30,791] [INFO] Running command: hmmsearch --tblout GCF_007095465.1_ASM709546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference/reference_markers.hmm GCF_007095465.1_ASM709546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:31,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:31,034] [INFO] Found 6/6 markers.
[2024-01-24 13:19:31,060] [INFO] Query marker FASTA was written to GCF_007095465.1_ASM709546v1_genomic.fna/markers.fasta
[2024-01-24 13:19:31,060] [INFO] Task started: Blastn
[2024-01-24 13:19:31,061] [INFO] Running command: blastn -query GCF_007095465.1_ASM709546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference/reference_markers.fasta -out GCF_007095465.1_ASM709546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:31,661] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:31,664] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:31,665] [INFO] Target genome list was writen to GCF_007095465.1_ASM709546v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:31,694] [INFO] Task started: fastANI
[2024-01-24 13:19:31,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg757edc6c-ff1e-42cf-9e65-8dcd62dd8ca3/GCF_007095465.1_ASM709546v1_genomic.fna.gz --refList GCF_007095465.1_ASM709546v1_genomic.fna/target_genomes.txt --output GCF_007095465.1_ASM709546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:35,366] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:35,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:35,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:35,382] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:35,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:35,382] [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 mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	100.0	532	534	95	conclusive
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	88.4676	433	534	95	below_threshold
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	88.4109	423	534	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_000425905.1	116089	116089	type	True	83.4828	322	534	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_001435695.1	116089	116089	type	True	83.2771	323	534	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	78.5262	112	534	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	78.4904	110	534	95	below_threshold
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	77.7891	61	534	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	77.3116	90	534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:35,383] [INFO] DFAST Taxonomy check result was written to GCF_007095465.1_ASM709546v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:35,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:35,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:35,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference/checkm_data
[2024-01-24 13:19:35,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:35,412] [INFO] Task started: CheckM
[2024-01-24 13:19:35,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007095465.1_ASM709546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007095465.1_ASM709546v1_genomic.fna/checkm_input GCF_007095465.1_ASM709546v1_genomic.fna/checkm_result
[2024-01-24 13:19:52,379] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:52,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,402] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:52,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:52,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007095465.1_ASM709546v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:52,403] [INFO] Task started: Blastn
[2024-01-24 13:19:52,404] [INFO] Running command: blastn -query GCF_007095465.1_ASM709546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fef4429-aaf8-4498-8c81-9a22c3c5df09/dqc_reference/reference_markers_gtdb.fasta -out GCF_007095465.1_ASM709546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:53,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:53,162] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:53,162] [INFO] Target genome list was writen to GCF_007095465.1_ASM709546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:53,369] [INFO] Task started: fastANI
[2024-01-24 13:19:53,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg757edc6c-ff1e-42cf-9e65-8dcd62dd8ca3/GCF_007095465.1_ASM709546v1_genomic.fna.gz --refList GCF_007095465.1_ASM709546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007095465.1_ASM709546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:58,423] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,440] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:58,440] [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_007095465.1	s__Lactobacillus mulieris	100.0	532	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	conclusive
GCF_001436455.1	s__Lactobacillus jensenii	88.3886	424	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_000425905.1	s__Lactobacillus psittaci	83.5256	320	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001434975.1	s__Lactobacillus gallinarum	78.7876	120	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001434335.1	s__Lactobacillus kalixensis	78.6995	116	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591845.1	s__Lactobacillus acidophilus	78.6922	136	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_003423665.1	s__Lactobacillus rodentium	78.5856	104	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570935.1	s__Lactobacillus sp007570935	78.5605	129	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178475.1	s__Lactobacillus amylolyticus	78.5577	109	534	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	78.5103	129	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCA_014803895.1	s__Lactobacillus sp014803895	78.4781	107	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004009905.1	s__Lactobacillus xujianguonis	78.2932	128	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_000296835.1	s__Lactobacillus hominis	78.1707	115	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_002916935.1	s__Lactobacillus panisapium	78.0234	77	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	77.6515	68	534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,442] [INFO] GTDB search result was written to GCF_007095465.1_ASM709546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:58,442] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:58,446] [INFO] DFAST_QC result json was written to GCF_007095465.1_ASM709546v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:58,446] [INFO] DFAST_QC completed!
[2024-01-24 13:19:58,447] [INFO] Total running time: 0h0m32s