[2024-01-24 13:57:41,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference
[2024-01-24 13:57:43,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,095] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,096] [INFO] Running command: gunzip -c /var/lib/cwl/stga99a294c-cbca-482d-b21d-4325442f7ec6/GCF_005405445.1_ASM540544v1_genomic.fna.gz | prodigal -d GCF_005405445.1_ASM540544v1_genomic.fna/cds.fna -a GCF_005405445.1_ASM540544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:47,496] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:47,496] [INFO] Task started: HMMsearch
[2024-01-24 13:57:47,496] [INFO] Running command: hmmsearch --tblout GCF_005405445.1_ASM540544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference/reference_markers.hmm GCF_005405445.1_ASM540544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:47,742] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:47,743] [INFO] Found 6/6 markers.
[2024-01-24 13:57:47,767] [INFO] Query marker FASTA was written to GCF_005405445.1_ASM540544v1_genomic.fna/markers.fasta
[2024-01-24 13:57:47,768] [INFO] Task started: Blastn
[2024-01-24 13:57:47,768] [INFO] Running command: blastn -query GCF_005405445.1_ASM540544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference/reference_markers.fasta -out GCF_005405445.1_ASM540544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:48,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:48,391] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:48,391] [INFO] Target genome list was writen to GCF_005405445.1_ASM540544v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:48,399] [INFO] Task started: fastANI
[2024-01-24 13:57:48,400] [INFO] Running command: fastANI --query /var/lib/cwl/stga99a294c-cbca-482d-b21d-4325442f7ec6/GCF_005405445.1_ASM540544v1_genomic.fna.gz --refList GCF_005405445.1_ASM540544v1_genomic.fna/target_genomes.txt --output GCF_005405445.1_ASM540544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:56,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:56,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:56,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:56,456] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:56,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:56,456] [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 nenjiangensis	strain=11102	GCA_005405445.1	1296540	1296540	type	True	100.0	604	607	95	conclusive
Paucilactobacillus oligofermentans	strain=DSM 15707	GCA_001434315.1	293371	293371	type	True	80.9051	335	607	95	below_threshold
Paucilactobacillus kaifaensis	strain=778-3	GCA_005405145.1	2559921	2559921	type	True	78.2147	97	607	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=LOOC260	GCA_000829395.1	1193095	1193095	type	True	77.783	123	607	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=DSM 26202	GCA_001437505.1	1193095	1193095	type	True	77.6691	117	607	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=JCM 18461	GCA_001311505.1	1193095	1193095	type	True	77.6585	123	607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:56,458] [INFO] DFAST Taxonomy check result was written to GCF_005405445.1_ASM540544v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:56,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:56,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:56,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference/checkm_data
[2024-01-24 13:57:56,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:56,492] [INFO] Task started: CheckM
[2024-01-24 13:57:56,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405445.1_ASM540544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405445.1_ASM540544v1_genomic.fna/checkm_input GCF_005405445.1_ASM540544v1_genomic.fna/checkm_result
[2024-01-24 13:58:17,851] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:17,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,872] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:17,872] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:17,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405445.1_ASM540544v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:17,873] [INFO] Task started: Blastn
[2024-01-24 13:58:17,873] [INFO] Running command: blastn -query GCF_005405445.1_ASM540544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf1c63d3-bab1-4fbe-ad19-3b5a9b666925/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405445.1_ASM540544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:18,753] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:18,757] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:18,757] [INFO] Target genome list was writen to GCF_005405445.1_ASM540544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:18,783] [INFO] Task started: fastANI
[2024-01-24 13:58:18,783] [INFO] Running command: fastANI --query /var/lib/cwl/stga99a294c-cbca-482d-b21d-4325442f7ec6/GCF_005405445.1_ASM540544v1_genomic.fna.gz --refList GCF_005405445.1_ASM540544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405445.1_ASM540544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:25,785] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:25,790] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:25,790] [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_005405445.1	s__Paucilactobacillus nenjiangensis	100.0	604	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	98.54	98.54	0.92	0.92	2	conclusive
GCF_001434315.1	s__Paucilactobacillus oligofermentans	80.9243	334	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005405145.1	s__Paucilactobacillus kaifaensis	78.2147	97	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829395.1	s__Paucilactobacillus hokkaidonensis	77.8102	122	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Paucilactobacillus	95.0	99.93	99.87	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,792] [INFO] GTDB search result was written to GCF_005405445.1_ASM540544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:25,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:25,796] [INFO] DFAST_QC result json was written to GCF_005405445.1_ASM540544v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:25,797] [INFO] DFAST_QC completed!
[2024-01-24 13:58:25,797] [INFO] Total running time: 0h0m44s