[2023-06-13 10:11:31,571] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:11:31,573] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:11:31,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference
[2023-06-13 10:11:32,800] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:11:32,801] [INFO] Task started: Prodigal
[2023-06-13 10:11:32,801] [INFO] Running command: gunzip -c /var/lib/cwl/stga610c996-e38c-4174-8168-692947ac8632/GCA_022713545.1_ASM2271354v1_genomic.fna.gz | prodigal -d GCA_022713545.1_ASM2271354v1_genomic.fna/cds.fna -a GCA_022713545.1_ASM2271354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:11:37,800] [INFO] Task succeeded: Prodigal
[2023-06-13 10:11:37,801] [INFO] Task started: HMMsearch
[2023-06-13 10:11:37,801] [INFO] Running command: hmmsearch --tblout GCA_022713545.1_ASM2271354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference/reference_markers.hmm GCA_022713545.1_ASM2271354v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:11:38,010] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:11:38,011] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga610c996-e38c-4174-8168-692947ac8632/GCA_022713545.1_ASM2271354v1_genomic.fna.gz]
[2023-06-13 10:11:38,031] [INFO] Query marker FASTA was written to GCA_022713545.1_ASM2271354v1_genomic.fna/markers.fasta
[2023-06-13 10:11:38,031] [INFO] Task started: Blastn
[2023-06-13 10:11:38,032] [INFO] Running command: blastn -query GCA_022713545.1_ASM2271354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference/reference_markers.fasta -out GCA_022713545.1_ASM2271354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:38,846] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:38,850] [INFO] Selected 16 target genomes.
[2023-06-13 10:11:38,850] [INFO] Target genome list was writen to GCA_022713545.1_ASM2271354v1_genomic.fna/target_genomes.txt
[2023-06-13 10:11:38,854] [INFO] Task started: fastANI
[2023-06-13 10:11:38,854] [INFO] Running command: fastANI --query /var/lib/cwl/stga610c996-e38c-4174-8168-692947ac8632/GCA_022713545.1_ASM2271354v1_genomic.fna.gz --refList GCA_022713545.1_ASM2271354v1_genomic.fna/target_genomes.txt --output GCA_022713545.1_ASM2271354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:44,901] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:44,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:44,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:44,914] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 10:11:44,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 10:11:44,914] [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 breve	strain=NCTC11815	GCA_900637145.1	1685	1685	type	True	98.3418	313	375	95	conclusive
Bifidobacterium breve	strain=JCM 1192	GCA_001025175.1	1685	1685	type	True	98.3415	313	375	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000771305.1	1685	1685	type	True	98.3408	311	375	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000158015.1	1685	1685	type	True	98.2371	313	375	95	conclusive
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	84.8948	246	375	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	84.6253	249	375	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	83.9227	239	375	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	83.9181	239	375	95	below_threshold
Bifidobacterium longum subsp. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	83.8801	245	375	95	below_threshold
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	83.8139	241	375	95	below_threshold
Bifidobacterium longum subsp. longum	strain=LMG 13197	GCA_000741245.1	1679	216816	type	True	83.7945	242	375	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.3663	218	375	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.3774	141	375	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.0218	69	375	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:11:44,916] [INFO] DFAST Taxonomy check result was written to GCA_022713545.1_ASM2271354v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:44,917] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:44,917] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:44,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference/checkm_data
[2023-06-13 10:11:44,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:44,940] [INFO] Task started: CheckM
[2023-06-13 10:11:44,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022713545.1_ASM2271354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022713545.1_ASM2271354v1_genomic.fna/checkm_input GCA_022713545.1_ASM2271354v1_genomic.fna/checkm_result
[2023-06-13 10:12:06,326] [INFO] Task succeeded: CheckM
[2023-06-13 10:12:06,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.52%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:12:06,355] [INFO] ===== Completeness check finished =====
[2023-06-13 10:12:06,356] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:12:06,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022713545.1_ASM2271354v1_genomic.fna/markers.fasta)
[2023-06-13 10:12:06,357] [INFO] Task started: Blastn
[2023-06-13 10:12:06,357] [INFO] Running command: blastn -query GCA_022713545.1_ASM2271354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff6ffd7-0e73-4666-8f59-520b5b7415b5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022713545.1_ASM2271354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:12:07,544] [INFO] Task succeeded: Blastn
[2023-06-13 10:12:07,555] [INFO] Selected 11 target genomes.
[2023-06-13 10:12:07,555] [INFO] Target genome list was writen to GCA_022713545.1_ASM2271354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:12:07,561] [INFO] Task started: fastANI
[2023-06-13 10:12:07,561] [INFO] Running command: fastANI --query /var/lib/cwl/stga610c996-e38c-4174-8168-692947ac8632/GCA_022713545.1_ASM2271354v1_genomic.fna.gz --refList GCA_022713545.1_ASM2271354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022713545.1_ASM2271354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:12:12,129] [INFO] Task succeeded: fastANI
[2023-06-13 10:12:12,143] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:12:12,143] [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_001025175.1	s__Bifidobacterium breve	98.2652	314	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	conclusive
GCF_000269965.1	s__Bifidobacterium infantis	84.8923	257	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_000196555.1	s__Bifidobacterium longum	83.9574	238	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.4972	219	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555355.1	s__Bifidobacterium sp018555355	81.2888	221	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_009193305.1	s__Bifidobacterium cebidarum	80.8606	192	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555455.1	s__Bifidobacterium sp018555455	80.7319	203	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802865.1	s__Bifidobacterium scaligerum	80.4228	185	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932375.1	s__Bifidobacterium sp012932375	80.4025	189	375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932425.1	s__Bifidobacterium sp012932425	79.7329	161	375	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 10:12:12,145] [INFO] GTDB search result was written to GCA_022713545.1_ASM2271354v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:12:12,145] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:12:12,149] [INFO] DFAST_QC result json was written to GCA_022713545.1_ASM2271354v1_genomic.fna/dqc_result.json
[2023-06-13 10:12:12,149] [INFO] DFAST_QC completed!
[2023-06-13 10:12:12,149] [INFO] Total running time: 0h0m41s