[2023-06-13 11:30:02,556] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:30:02,562] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:30:02,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference
[2023-06-13 11:30:03,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:30:03,957] [INFO] Task started: Prodigal
[2023-06-13 11:30:03,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e0451a0-27ae-4650-8c94-3c063598368d/GCA_022738165.1_ASM2273816v1_genomic.fna.gz | prodigal -d GCA_022738165.1_ASM2273816v1_genomic.fna/cds.fna -a GCA_022738165.1_ASM2273816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:30:09,950] [INFO] Task succeeded: Prodigal
[2023-06-13 11:30:09,950] [INFO] Task started: HMMsearch
[2023-06-13 11:30:09,950] [INFO] Running command: hmmsearch --tblout GCA_022738165.1_ASM2273816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference/reference_markers.hmm GCA_022738165.1_ASM2273816v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:30:10,213] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:30:10,214] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e0451a0-27ae-4650-8c94-3c063598368d/GCA_022738165.1_ASM2273816v1_genomic.fna.gz]
[2023-06-13 11:30:10,235] [INFO] Query marker FASTA was written to GCA_022738165.1_ASM2273816v1_genomic.fna/markers.fasta
[2023-06-13 11:30:10,236] [INFO] Task started: Blastn
[2023-06-13 11:30:10,236] [INFO] Running command: blastn -query GCA_022738165.1_ASM2273816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference/reference_markers.fasta -out GCA_022738165.1_ASM2273816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:11,126] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:11,129] [INFO] Selected 10 target genomes.
[2023-06-13 11:30:11,130] [INFO] Target genome list was writen to GCA_022738165.1_ASM2273816v1_genomic.fna/target_genomes.txt
[2023-06-13 11:30:11,131] [INFO] Task started: fastANI
[2023-06-13 11:30:11,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e0451a0-27ae-4650-8c94-3c063598368d/GCA_022738165.1_ASM2273816v1_genomic.fna.gz --refList GCA_022738165.1_ASM2273816v1_genomic.fna/target_genomes.txt --output GCA_022738165.1_ASM2273816v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:16,179] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:16,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:16,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:16,187] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 11:30:16,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:30:16,188] [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
Bifidobacterium longum subsp. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	98.6981	500	540	95	conclusive
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	98.6512	500	540	95	conclusive
Bifidobacterium longum subsp. longum	strain=LMG 13197	GCA_000741245.1	1679	216816	type	True	98.5568	506	540	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	98.5507	506	540	95	conclusive
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	98.5502	506	540	95	conclusive
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.7927	391	540	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.1862	97	540	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:30:16,190] [INFO] DFAST Taxonomy check result was written to GCA_022738165.1_ASM2273816v1_genomic.fna/tc_result.tsv
[2023-06-13 11:30:16,190] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:16,191] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:16,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference/checkm_data
[2023-06-13 11:30:16,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:16,220] [INFO] Task started: CheckM
[2023-06-13 11:30:16,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022738165.1_ASM2273816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022738165.1_ASM2273816v1_genomic.fna/checkm_input GCA_022738165.1_ASM2273816v1_genomic.fna/checkm_result
[2023-06-13 11:30:40,622] [INFO] Task succeeded: CheckM
[2023-06-13 11:30:40,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.04%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 11:30:40,646] [INFO] ===== Completeness check finished =====
[2023-06-13 11:30:40,646] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:30:40,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022738165.1_ASM2273816v1_genomic.fna/markers.fasta)
[2023-06-13 11:30:40,647] [INFO] Task started: Blastn
[2023-06-13 11:30:40,647] [INFO] Running command: blastn -query GCA_022738165.1_ASM2273816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48a89267-a8d4-4d73-bd3f-0ce9eed2c2d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022738165.1_ASM2273816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:41,829] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:41,835] [INFO] Selected 7 target genomes.
[2023-06-13 11:30:41,835] [INFO] Target genome list was writen to GCA_022738165.1_ASM2273816v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:30:41,838] [INFO] Task started: fastANI
[2023-06-13 11:30:41,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e0451a0-27ae-4650-8c94-3c063598368d/GCA_022738165.1_ASM2273816v1_genomic.fna.gz --refList GCA_022738165.1_ASM2273816v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022738165.1_ASM2273816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:30:45,790] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:45,801] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:30:45,801] [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_000196555.1	s__Bifidobacterium longum	98.5507	506	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	conclusive
GCF_000269965.1	s__Bifidobacterium infantis	94.9793	447	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_001025175.1	s__Bifidobacterium breve	86.5455	405	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_018555355.1	s__Bifidobacterium sp018555355	83.6912	400	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	83.5552	394	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259745.1	s__Bifidobacterium myosotis	82.9624	377	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_012932425.1	s__Bifidobacterium sp012932425	80.9496	308	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:30:45,803] [INFO] GTDB search result was written to GCA_022738165.1_ASM2273816v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:30:45,804] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:30:45,808] [INFO] DFAST_QC result json was written to GCA_022738165.1_ASM2273816v1_genomic.fna/dqc_result.json
[2023-06-13 11:30:45,808] [INFO] DFAST_QC completed!
[2023-06-13 11:30:45,808] [INFO] Total running time: 0h0m43s