[2024-01-25 19:39:35,682] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:35,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:35,684] [INFO] DQC Reference Directory: /var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference
[2024-01-25 19:39:36,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:36,837] [INFO] Task started: Prodigal
[2024-01-25 19:39:36,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ef6671e-1dc7-4052-9439-61ea2de60a31/GCF_002849515.1_ASM284951v1_genomic.fna.gz | prodigal -d GCF_002849515.1_ASM284951v1_genomic.fna/cds.fna -a GCF_002849515.1_ASM284951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:43,541] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:43,542] [INFO] Task started: HMMsearch
[2024-01-25 19:39:43,542] [INFO] Running command: hmmsearch --tblout GCF_002849515.1_ASM284951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference/reference_markers.hmm GCF_002849515.1_ASM284951v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:43,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:43,753] [INFO] Found 6/6 markers.
[2024-01-25 19:39:43,776] [INFO] Query marker FASTA was written to GCF_002849515.1_ASM284951v1_genomic.fna/markers.fasta
[2024-01-25 19:39:43,777] [INFO] Task started: Blastn
[2024-01-25 19:39:43,777] [INFO] Running command: blastn -query GCF_002849515.1_ASM284951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference/reference_markers.fasta -out GCF_002849515.1_ASM284951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:44,320] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:44,322] [INFO] Selected 17 target genomes.
[2024-01-25 19:39:44,323] [INFO] Target genome list was writen to GCF_002849515.1_ASM284951v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:44,341] [INFO] Task started: fastANI
[2024-01-25 19:39:44,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef6671e-1dc7-4052-9439-61ea2de60a31/GCF_002849515.1_ASM284951v1_genomic.fna.gz --refList GCF_002849515.1_ASM284951v1_genomic.fna/target_genomes.txt --output GCF_002849515.1_ASM284951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:55,943] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:55,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:55,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:55,950] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:39:55,950] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:55,950] [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=NRRL B-442	GCA_002849515.1	47715	47715	type	True	100.0	966	967	95	conclusive
Lacticaseibacillus rhamnosus	strain=NCTC13764	GCA_900636965.1	47715	47715	type	True	99.9883	966	967	95	conclusive
Lacticaseibacillus rhamnosus	strain=DSM 20021	GCA_001435405.1	47715	47715	type	True	99.9804	957	967	95	conclusive
Lacticaseibacillus rhamnosus	strain=NBRC 3425	GCA_007990855.1	47715	47715	type	True	99.8491	859	967	95	conclusive
Lacticaseibacillus zeae	strain=KCTC 3804	GCA_000260435.1	57037	57037	type	True	81.0099	534	967	95	below_threshold
Lacticaseibacillus chiayiensis	strain=NCYUAS	GCA_004123795.1	2100821	2100821	type	True	80.6529	501	967	95	below_threshold
Lacticaseibacillus mingshuiensis	strain=117-1	GCA_016861785.1	2799574	2799574	type	True	78.3567	55	967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:55,952] [INFO] DFAST Taxonomy check result was written to GCF_002849515.1_ASM284951v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:55,952] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:55,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:55,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference/checkm_data
[2024-01-25 19:39:55,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:55,998] [INFO] Task started: CheckM
[2024-01-25 19:39:55,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002849515.1_ASM284951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002849515.1_ASM284951v1_genomic.fna/checkm_input GCF_002849515.1_ASM284951v1_genomic.fna/checkm_result
[2024-01-25 19:40:21,288] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:21,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:21,315] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:21,315] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:21,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002849515.1_ASM284951v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:21,316] [INFO] Task started: Blastn
[2024-01-25 19:40:21,316] [INFO] Running command: blastn -query GCF_002849515.1_ASM284951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc494b80c-5b07-459f-af07-5e55b5b7d949/dqc_reference/reference_markers_gtdb.fasta -out GCF_002849515.1_ASM284951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:22,051] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:22,055] [INFO] Selected 17 target genomes.
[2024-01-25 19:40:22,055] [INFO] Target genome list was writen to GCF_002849515.1_ASM284951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:22,068] [INFO] Task started: fastANI
[2024-01-25 19:40:22,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef6671e-1dc7-4052-9439-61ea2de60a31/GCF_002849515.1_ASM284951v1_genomic.fna.gz --refList GCF_002849515.1_ASM284951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002849515.1_ASM284951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:31,086] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:31,091] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:31,092] [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	99.9883	966	967	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_000829055.1	s__Lacticaseibacillus casei	81.0203	519	967	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.76	95.69	0.93	0.80	19	-
GCF_000260435.1	s__Lacticaseibacillus zeae	81.0015	537	967	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.07	96.92	0.91	0.87	11	-
GCF_004123795.1	s__Lacticaseibacillus chiayiensis	80.6899	500	967	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	80.0067	424	967	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	78.693	54	967	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	77.6418	58	967	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:31,093] [INFO] GTDB search result was written to GCF_002849515.1_ASM284951v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:31,093] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:31,096] [INFO] DFAST_QC result json was written to GCF_002849515.1_ASM284951v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:31,096] [INFO] DFAST_QC completed!
[2024-01-25 19:40:31,096] [INFO] Total running time: 0h0m55s