[2024-01-24 14:55:18,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:18,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:18,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference
[2024-01-24 14:55:19,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:19,608] [INFO] Task started: Prodigal
[2024-01-24 14:55:19,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bc0b853-4d60-461f-85fa-f9d7b33fac0b/GCF_000236455.2_ASM23645v2_genomic.fna.gz | prodigal -d GCF_000236455.2_ASM23645v2_genomic.fna/cds.fna -a GCF_000236455.2_ASM23645v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:24,075] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:24,075] [INFO] Task started: HMMsearch
[2024-01-24 14:55:24,075] [INFO] Running command: hmmsearch --tblout GCF_000236455.2_ASM23645v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference/reference_markers.hmm GCF_000236455.2_ASM23645v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:24,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:24,313] [INFO] Found 6/6 markers.
[2024-01-24 14:55:24,336] [INFO] Query marker FASTA was written to GCF_000236455.2_ASM23645v2_genomic.fna/markers.fasta
[2024-01-24 14:55:24,336] [INFO] Task started: Blastn
[2024-01-24 14:55:24,336] [INFO] Running command: blastn -query GCF_000236455.2_ASM23645v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference/reference_markers.fasta -out GCF_000236455.2_ASM23645v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:24,931] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:24,935] [INFO] Selected 12 target genomes.
[2024-01-24 14:55:24,936] [INFO] Target genome list was writen to GCF_000236455.2_ASM23645v2_genomic.fna/target_genomes.txt
[2024-01-24 14:55:24,952] [INFO] Task started: fastANI
[2024-01-24 14:55:24,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc0b853-4d60-461f-85fa-f9d7b33fac0b/GCF_000236455.2_ASM23645v2_genomic.fna.gz --refList GCF_000236455.2_ASM23645v2_genomic.fna/target_genomes.txt --output GCF_000236455.2_ASM23645v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:32,265] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:32,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:32,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:32,273] [INFO] Found 7 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:55:32,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:32,274] [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
Limosilactobacillus reuteri subsp. suis	strain=ATCC 53608	GCA_000236455.2	927703	1598	type	True	100.0	695	696	95	conclusive
Limosilactobacillus reuteri subsp. rodentium	strain=100-23	GCA_000168255.1	349123	1598	type	True	96.2613	542	696	95	conclusive
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	95.9195	540	696	95	conclusive
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	95.9086	548	696	95	conclusive
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	95.7372	513	696	95	conclusive
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	95.1677	538	696	95	conclusive
Limosilactobacillus balticus	strain=BG-AF3-A	GCA_014145615.1	2759747	2759747	type	True	93.8732	535	696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:32,275] [INFO] DFAST Taxonomy check result was written to GCF_000236455.2_ASM23645v2_genomic.fna/tc_result.tsv
[2024-01-24 14:55:32,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:32,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:32,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference/checkm_data
[2024-01-24 14:55:32,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:32,304] [INFO] Task started: CheckM
[2024-01-24 14:55:32,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000236455.2_ASM23645v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000236455.2_ASM23645v2_genomic.fna/checkm_input GCF_000236455.2_ASM23645v2_genomic.fna/checkm_result
[2024-01-24 14:55:53,946] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:53,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:53,985] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:53,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:53,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000236455.2_ASM23645v2_genomic.fna/markers.fasta)
[2024-01-24 14:55:53,987] [INFO] Task started: Blastn
[2024-01-24 14:55:53,987] [INFO] Running command: blastn -query GCF_000236455.2_ASM23645v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd233ad6a-9afe-4654-bb66-4ea1206daf2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000236455.2_ASM23645v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:54,809] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:54,813] [INFO] Selected 5 target genomes.
[2024-01-24 14:55:54,813] [INFO] Target genome list was writen to GCF_000236455.2_ASM23645v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:54,820] [INFO] Task started: fastANI
[2024-01-24 14:55:54,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc0b853-4d60-461f-85fa-f9d7b33fac0b/GCF_000236455.2_ASM23645v2_genomic.fna.gz --refList GCF_000236455.2_ASM23645v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000236455.2_ASM23645v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:58,576] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:58,587] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:55:58,588] [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_000016825.1	s__Limosilactobacillus reuteri	95.9158	541	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	inconclusive
GCA_003072625.1	s__Limosilactobacillus reuteri_D	95.1936	541	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	inconclusive
GCF_013694365.1	s__Limosilactobacillus reuteri_E	94.1344	525	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.28	96.40	0.80	0.72	58	-
GCF_014145615.1	s__Limosilactobacillus balticus	93.8786	535	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.51	98.51	0.89	0.89	2	-
GCF_014145585.1	s__Limosilactobacillus agrestis	90.588	478	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.60	98.25	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:58,589] [INFO] GTDB search result was written to GCF_000236455.2_ASM23645v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:58,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:58,593] [INFO] DFAST_QC result json was written to GCF_000236455.2_ASM23645v2_genomic.fna/dqc_result.json
[2024-01-24 14:55:58,593] [INFO] DFAST_QC completed!
[2024-01-24 14:55:58,593] [INFO] Total running time: 0h0m40s