[2024-01-24 13:45:57,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:57,993] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:57,993] [INFO] DQC Reference Directory: /var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference
[2024-01-24 13:45:59,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:59,324] [INFO] Task started: Prodigal
[2024-01-24 13:45:59,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dda7e58-d8ce-49c8-9f28-239820ea06ee/GCF_000377985.1_ASM37798v1_genomic.fna.gz | prodigal -d GCF_000377985.1_ASM37798v1_genomic.fna/cds.fna -a GCF_000377985.1_ASM37798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:06,353] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:06,354] [INFO] Task started: HMMsearch
[2024-01-24 13:46:06,354] [INFO] Running command: hmmsearch --tblout GCF_000377985.1_ASM37798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference/reference_markers.hmm GCF_000377985.1_ASM37798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:06,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:06,606] [INFO] Found 6/6 markers.
[2024-01-24 13:46:06,635] [INFO] Query marker FASTA was written to GCF_000377985.1_ASM37798v1_genomic.fna/markers.fasta
[2024-01-24 13:46:06,636] [INFO] Task started: Blastn
[2024-01-24 13:46:06,636] [INFO] Running command: blastn -query GCF_000377985.1_ASM37798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference/reference_markers.fasta -out GCF_000377985.1_ASM37798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:07,237] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:07,241] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:07,241] [INFO] Target genome list was writen to GCF_000377985.1_ASM37798v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:07,297] [INFO] Task started: fastANI
[2024-01-24 13:46:07,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dda7e58-d8ce-49c8-9f28-239820ea06ee/GCF_000377985.1_ASM37798v1_genomic.fna.gz --refList GCF_000377985.1_ASM37798v1_genomic.fna/target_genomes.txt --output GCF_000377985.1_ASM37798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:16,446] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:16,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:16,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:16,454] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:16,455] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:16,455] [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
Sporolactobacillus vineae	strain=DSM 21990	GCA_000377985.1	444463	444463	type	True	100.0	928	931	95	conclusive
Sporolactobacillus vineae	strain=SL153	GCA_000246965.2	444463	444463	type	True	99.9672	905	931	95	conclusive
Sporolactobacillus shoreae	strain=BK92	GCA_004684935.1	1465501	1465501	type	True	78.2073	218	931	95	below_threshold
Sporolactobacillus pectinivorans	strain=GD201205	GCA_002802965.1	1591408	1591408	type	True	77.7608	186	931	95	below_threshold
Sporolactobacillus inulinus	strain=NBRC 13595	GCA_006539285.1	2078	2078	type	True	77.4687	95	931	95	below_threshold
Sporolactobacillus spathodeae	strain=DSM 100968	GCA_016908935.1	1465502	1465502	type	True	77.4216	104	931	95	below_threshold
Sporolactobacillus terrae	strain=DSM 11697	GCA_000648615.1	269673	269673	type	True	77.4037	108	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:16,456] [INFO] DFAST Taxonomy check result was written to GCF_000377985.1_ASM37798v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:16,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:16,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:16,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference/checkm_data
[2024-01-24 13:46:16,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:16,493] [INFO] Task started: CheckM
[2024-01-24 13:46:16,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000377985.1_ASM37798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000377985.1_ASM37798v1_genomic.fna/checkm_input GCF_000377985.1_ASM37798v1_genomic.fna/checkm_result
[2024-01-24 13:46:45,989] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:45,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:46,010] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:46,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:46,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000377985.1_ASM37798v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:46,012] [INFO] Task started: Blastn
[2024-01-24 13:46:46,012] [INFO] Running command: blastn -query GCF_000377985.1_ASM37798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd94e81f4-9b6b-46bd-9067-85facfb778ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_000377985.1_ASM37798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:46,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:46,863] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:46,863] [INFO] Target genome list was writen to GCF_000377985.1_ASM37798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:46,895] [INFO] Task started: fastANI
[2024-01-24 13:46:46,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dda7e58-d8ce-49c8-9f28-239820ea06ee/GCF_000377985.1_ASM37798v1_genomic.fna.gz --refList GCF_000377985.1_ASM37798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000377985.1_ASM37798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:02,091] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:02,103] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:02,103] [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_000377985.1	s__Sporolactobacillus vineae	100.0	928	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_004153195.1	s__Sporolactobacillus sp004153195	78.3849	161	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684935.1	s__Sporolactobacillus shoreae	78.2233	217	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802965.1	s__Sporolactobacillus pectinivorans	77.7608	186	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539285.1	s__Sporolactobacillus inulinus	77.4687	95	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	99.52	99.06	0.91	0.89	3	-
GCF_016908935.1	s__Sporolactobacillus spathodeae	77.4482	105	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000648615.1	s__Sporolactobacillus terrae	77.4037	108	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	98.89	98.59	0.91	0.87	6	-
GCF_004153165.1	s__Sporolactobacillus sp004153165	77.3999	107	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647035.1	s__Sporolactobacillus putidus	77.377	157	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543345.1	s__Sporolactobacillus sp900543345	76.7161	94	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,105] [INFO] GTDB search result was written to GCF_000377985.1_ASM37798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:02,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:02,109] [INFO] DFAST_QC result json was written to GCF_000377985.1_ASM37798v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:02,110] [INFO] DFAST_QC completed!
[2024-01-24 13:47:02,110] [INFO] Total running time: 0h1m4s