[2024-01-24 13:40:30,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,236] [INFO] DQC Reference Directory: /var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference
[2024-01-24 13:40:31,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,559] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg920e2b0d-e86a-4a27-82ca-518396eb7e85/GCF_005405145.1_ASM540514v1_genomic.fna.gz | prodigal -d GCF_005405145.1_ASM540514v1_genomic.fna/cds.fna -a GCF_005405145.1_ASM540514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:35,374] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:35,375] [INFO] Task started: HMMsearch
[2024-01-24 13:40:35,375] [INFO] Running command: hmmsearch --tblout GCF_005405145.1_ASM540514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference/reference_markers.hmm GCF_005405145.1_ASM540514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:35,595] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:35,596] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg920e2b0d-e86a-4a27-82ca-518396eb7e85/GCF_005405145.1_ASM540514v1_genomic.fna.gz]
[2024-01-24 13:40:35,618] [INFO] Query marker FASTA was written to GCF_005405145.1_ASM540514v1_genomic.fna/markers.fasta
[2024-01-24 13:40:35,619] [INFO] Task started: Blastn
[2024-01-24 13:40:35,619] [INFO] Running command: blastn -query GCF_005405145.1_ASM540514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference/reference_markers.fasta -out GCF_005405145.1_ASM540514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:36,259] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:36,263] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:36,264] [INFO] Target genome list was writen to GCF_005405145.1_ASM540514v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:36,274] [INFO] Task started: fastANI
[2024-01-24 13:40:36,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg920e2b0d-e86a-4a27-82ca-518396eb7e85/GCF_005405145.1_ASM540514v1_genomic.fna.gz --refList GCF_005405145.1_ASM540514v1_genomic.fna/target_genomes.txt --output GCF_005405145.1_ASM540514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:41,754] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:41,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:41,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:41,764] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:41,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:41,764] [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
Paucilactobacillus kaifaensis	strain=778-3	GCA_005405145.1	2559921	2559921	type	True	100.0	558	562	95	conclusive
Paucilactobacillus hokkaidonensis	strain=LOOC260	GCA_000829395.1	1193095	1193095	type	True	80.5294	331	562	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=DSM 26202	GCA_001437505.1	1193095	1193095	type	True	80.246	323	562	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=JCM 18461	GCA_001311505.1	1193095	1193095	type	True	80.2354	325	562	95	below_threshold
Paucilactobacillus wasatchensis	strain=WDC04	GCA_000876205.1	1335616	1335616	type	True	79.6175	240	562	95	below_threshold
Pediococcus inopinatus	strain=DSM 20285	GCA_001438725.1	114090	114090	type	True	79.2152	53	562	95	below_threshold
Pediococcus inopinatus	strain=DSM 20285	GCA_002982135.1	114090	114090	type	True	79.1003	56	562	95	below_threshold
Paucilactobacillus nenjiangensis	strain=11102	GCA_005405445.1	1296540	1296540	type	True	78.339	98	562	95	below_threshold
Paucilactobacillus oligofermentans	strain=DSM 15707	GCA_001434315.1	293371	293371	type	True	77.5942	93	562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:41,766] [INFO] DFAST Taxonomy check result was written to GCF_005405145.1_ASM540514v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:41,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:41,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:41,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference/checkm_data
[2024-01-24 13:40:41,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:41,792] [INFO] Task started: CheckM
[2024-01-24 13:40:41,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405145.1_ASM540514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405145.1_ASM540514v1_genomic.fna/checkm_input GCF_005405145.1_ASM540514v1_genomic.fna/checkm_result
[2024-01-24 13:41:01,434] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:01,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,502] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:01,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:01,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405145.1_ASM540514v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:01,504] [INFO] Task started: Blastn
[2024-01-24 13:41:01,504] [INFO] Running command: blastn -query GCF_005405145.1_ASM540514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6d3eea3-109b-43d3-8219-e5c995f48867/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405145.1_ASM540514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,369] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:02,370] [INFO] Target genome list was writen to GCF_005405145.1_ASM540514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:02,400] [INFO] Task started: fastANI
[2024-01-24 13:41:02,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg920e2b0d-e86a-4a27-82ca-518396eb7e85/GCF_005405145.1_ASM540514v1_genomic.fna.gz --refList GCF_005405145.1_ASM540514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405145.1_ASM540514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:11,483] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:11,497] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:11,497] [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_005405145.1	s__Paucilactobacillus kaifaensis	100.0	558	562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000829395.1	s__Paucilactobacillus hokkaidonensis	80.5294	331	562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	99.93	99.87	1.00	1.00	3	-
GCF_000876205.1	s__Paucilactobacillus wasatchensis	79.5958	241	562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982135.1	s__Pediococcus inopinatus	79.1023	56	562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.47	98.95	0.96	0.92	3	-
GCF_005405445.1	s__Paucilactobacillus nenjiangensis	78.339	98	562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	98.54	98.54	0.92	0.92	2	-
GCF_001434315.1	s__Paucilactobacillus oligofermentans	77.5942	93	562	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,499] [INFO] GTDB search result was written to GCF_005405145.1_ASM540514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:11,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:11,505] [INFO] DFAST_QC result json was written to GCF_005405145.1_ASM540514v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:11,505] [INFO] DFAST_QC completed!
[2024-01-24 13:41:11,506] [INFO] Total running time: 0h0m41s