[2024-01-24 10:57:38,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference
[2024-01-24 10:57:39,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,650] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a261170-acb2-429b-8094-8b163cb27dd1/GCF_001435655.1_ASM143565v1_genomic.fna.gz | prodigal -d GCF_001435655.1_ASM143565v1_genomic.fna/cds.fna -a GCF_001435655.1_ASM143565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:46,919] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:46,920] [INFO] Task started: HMMsearch
[2024-01-24 10:57:46,920] [INFO] Running command: hmmsearch --tblout GCF_001435655.1_ASM143565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference/reference_markers.hmm GCF_001435655.1_ASM143565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:47,156] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:47,157] [INFO] Found 6/6 markers.
[2024-01-24 10:57:47,190] [INFO] Query marker FASTA was written to GCF_001435655.1_ASM143565v1_genomic.fna/markers.fasta
[2024-01-24 10:57:47,191] [INFO] Task started: Blastn
[2024-01-24 10:57:47,191] [INFO] Running command: blastn -query GCF_001435655.1_ASM143565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference/reference_markers.fasta -out GCF_001435655.1_ASM143565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:47,779] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:47,782] [INFO] Selected 12 target genomes.
[2024-01-24 10:57:47,783] [INFO] Target genome list was writen to GCF_001435655.1_ASM143565v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:47,806] [INFO] Task started: fastANI
[2024-01-24 10:57:47,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a261170-acb2-429b-8094-8b163cb27dd1/GCF_001435655.1_ASM143565v1_genomic.fna.gz --refList GCF_001435655.1_ASM143565v1_genomic.fna/target_genomes.txt --output GCF_001435655.1_ASM143565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:55,716] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:55,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:55,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:55,730] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:55,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:55,731] [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
Lactiplantibacillus paraplantarum	strain=DSM 10667	GCA_001435655.1	60520	60520	type	True	100.0	1042	1046	95	conclusive
Lactiplantibacillus paraplantarum	strain=DSM 10667	GCA_003641145.1	60520	60520	type	True	99.961	1019	1046	95	conclusive
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	87.727	786	1046	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	87.6534	784	1046	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=NBRC 15891	GCA_007989145.1	337330	1590	type	True	87.5719	789	1046	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_001435215.1	271881	271881	type	True	87.255	760	1046	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	87.2326	801	1046	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:55,733] [INFO] DFAST Taxonomy check result was written to GCF_001435655.1_ASM143565v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:55,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:55,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:55,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference/checkm_data
[2024-01-24 10:57:55,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:55,773] [INFO] Task started: CheckM
[2024-01-24 10:57:55,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435655.1_ASM143565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435655.1_ASM143565v1_genomic.fna/checkm_input GCF_001435655.1_ASM143565v1_genomic.fna/checkm_result
[2024-01-24 10:58:23,949] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:23,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,974] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:23,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:23,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435655.1_ASM143565v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:23,976] [INFO] Task started: Blastn
[2024-01-24 10:58:23,976] [INFO] Running command: blastn -query GCF_001435655.1_ASM143565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg907afd3f-43d8-481e-8c26-61e8b8ef41bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435655.1_ASM143565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:24,748] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:24,753] [INFO] Selected 8 target genomes.
[2024-01-24 10:58:24,753] [INFO] Target genome list was writen to GCF_001435655.1_ASM143565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:24,760] [INFO] Task started: fastANI
[2024-01-24 10:58:24,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a261170-acb2-429b-8094-8b163cb27dd1/GCF_001435655.1_ASM143565v1_genomic.fna.gz --refList GCF_001435655.1_ASM143565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435655.1_ASM143565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:30,399] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:30,407] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:30,408] [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_003641145.1	s__Lactiplantibacillus paraplantarum	99.9363	1020	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.82	97.28	0.92	0.86	13	conclusive
GCF_014131735.1	s__Lactiplantibacillus plantarum	87.7172	787	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	-
GCF_003641185.1	s__Lactiplantibacillus pentosus	82.2456	645	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	82.2166	619	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.3668	372	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	79.6561	302	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005404945.1	s__Lactiplantibacillus pingfangensis	79.6005	299	1046	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:30,412] [INFO] GTDB search result was written to GCF_001435655.1_ASM143565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:30,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:30,417] [INFO] DFAST_QC result json was written to GCF_001435655.1_ASM143565v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:30,417] [INFO] DFAST_QC completed!
[2024-01-24 10:58:30,417] [INFO] Total running time: 0h0m52s