[2024-01-24 13:40:32,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:32,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:32,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference
[2024-01-24 13:40:34,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,008] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg17389b9c-6f60-475c-a22f-6af4d1d697f3/GCF_001435405.1_ASM143540v1_genomic.fna.gz | prodigal -d GCF_001435405.1_ASM143540v1_genomic.fna/cds.fna -a GCF_001435405.1_ASM143540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:41,709] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:41,709] [INFO] Task started: HMMsearch
[2024-01-24 13:40:41,709] [INFO] Running command: hmmsearch --tblout GCF_001435405.1_ASM143540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference/reference_markers.hmm GCF_001435405.1_ASM143540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:41,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:41,977] [INFO] Found 6/6 markers.
[2024-01-24 13:40:42,004] [INFO] Query marker FASTA was written to GCF_001435405.1_ASM143540v1_genomic.fna/markers.fasta
[2024-01-24 13:40:42,005] [INFO] Task started: Blastn
[2024-01-24 13:40:42,005] [INFO] Running command: blastn -query GCF_001435405.1_ASM143540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference/reference_markers.fasta -out GCF_001435405.1_ASM143540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,619] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,622] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:42,622] [INFO] Target genome list was writen to GCF_001435405.1_ASM143540v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:42,635] [INFO] Task started: fastANI
[2024-01-24 13:40:42,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg17389b9c-6f60-475c-a22f-6af4d1d697f3/GCF_001435405.1_ASM143540v1_genomic.fna.gz --refList GCF_001435405.1_ASM143540v1_genomic.fna/target_genomes.txt --output GCF_001435405.1_ASM143540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:53,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:53,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:53,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:53,888] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:40:53,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:53,889] [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
Lacticaseibacillus rhamnosus	strain=DSM 20021	GCA_001435405.1	47715	47715	type	True	100.0	963	966	95	conclusive
Lacticaseibacillus rhamnosus	strain=NCTC13764	GCA_900636965.1	47715	47715	type	True	99.9858	964	966	95	conclusive
Lacticaseibacillus rhamnosus	strain=NRRL B-442	GCA_002849515.1	47715	47715	type	True	99.9829	954	966	95	conclusive
Lacticaseibacillus rhamnosus	strain=NBRC 3425	GCA_007990855.1	47715	47715	type	True	99.8569	854	966	95	conclusive
Lacticaseibacillus zeae	strain=KCTC 3804	GCA_000260435.1	57037	57037	type	True	81.1414	519	966	95	below_threshold
Lacticaseibacillus chiayiensis	strain=NCYUAS	GCA_004123795.1	2100821	2100821	type	True	80.9241	494	966	95	below_threshold
Lacticaseibacillus mingshuiensis	strain=117-1	GCA_016861785.1	2799574	2799574	type	True	77.9014	57	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:53,890] [INFO] DFAST Taxonomy check result was written to GCF_001435405.1_ASM143540v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:53,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:53,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:53,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference/checkm_data
[2024-01-24 13:40:53,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:53,926] [INFO] Task started: CheckM
[2024-01-24 13:40:53,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435405.1_ASM143540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435405.1_ASM143540v1_genomic.fna/checkm_input GCF_001435405.1_ASM143540v1_genomic.fna/checkm_result
[2024-01-24 13:41:23,868] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:23,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:23,897] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:23,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:23,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435405.1_ASM143540v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:23,898] [INFO] Task started: Blastn
[2024-01-24 13:41:23,898] [INFO] Running command: blastn -query GCF_001435405.1_ASM143540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb068bfe4-f92b-490c-a550-da2055b3fa40/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435405.1_ASM143540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:24,752] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:24,756] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:24,757] [INFO] Target genome list was writen to GCF_001435405.1_ASM143540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:24,877] [INFO] Task started: fastANI
[2024-01-24 13:41:24,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg17389b9c-6f60-475c-a22f-6af4d1d697f3/GCF_001435405.1_ASM143540v1_genomic.fna.gz --refList GCF_001435405.1_ASM143540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435405.1_ASM143540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:34,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:34,729] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:34,729] [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_900636965.1	s__Lacticaseibacillus rhamnosus	99.9858	964	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.40	96.73	0.93	0.86	237	conclusive
GCF_000260435.1	s__Lacticaseibacillus zeae	81.1816	518	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.07	96.92	0.91	0.87	11	-
GCF_000829055.1	s__Lacticaseibacillus casei	81.1119	511	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.76	95.69	0.93	0.80	19	-
GCF_004123795.1	s__Lacticaseibacillus chiayiensis	80.9274	494	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.97	98.62	0.94	0.94	3	-
GCF_000829035.1	s__Lacticaseibacillus paracasei	79.8238	423	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.30	97.86	0.88	0.73	252	-
GCF_016861765.1	s__Lacticaseibacillus sp016861765	78.1505	52	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.52	99.51	0.95	0.95	3	-
GCF_003946465.1	s__Lacticaseibacillus hegangensis	77.4482	62	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:34,731] [INFO] GTDB search result was written to GCF_001435405.1_ASM143540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:34,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:34,734] [INFO] DFAST_QC result json was written to GCF_001435405.1_ASM143540v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:34,734] [INFO] DFAST_QC completed!
[2024-01-24 13:41:34,734] [INFO] Total running time: 0h1m2s