[2024-01-24 11:26:20,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,786] [INFO] DQC Reference Directory: /var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference
[2024-01-24 11:26:22,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,015] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,016] [INFO] Running command: gunzip -c /var/lib/cwl/stgc662708e-68e1-4e80-888d-14e1d1a65aea/GCF_000771285.1_DSM-20211_genomic.fna.gz | prodigal -d GCF_000771285.1_DSM-20211_genomic.fna/cds.fna -a GCF_000771285.1_DSM-20211_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:29,745] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:29,746] [INFO] Task started: HMMsearch
[2024-01-24 11:26:29,746] [INFO] Running command: hmmsearch --tblout GCF_000771285.1_DSM-20211_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference/reference_markers.hmm GCF_000771285.1_DSM-20211_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:29,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:30,000] [INFO] Found 6/6 markers.
[2024-01-24 11:26:30,026] [INFO] Query marker FASTA was written to GCF_000771285.1_DSM-20211_genomic.fna/markers.fasta
[2024-01-24 11:26:30,026] [INFO] Task started: Blastn
[2024-01-24 11:26:30,026] [INFO] Running command: blastn -query GCF_000771285.1_DSM-20211_genomic.fna/markers.fasta -db /var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference/reference_markers.fasta -out GCF_000771285.1_DSM-20211_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:30,962] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:30,966] [INFO] Selected 15 target genomes.
[2024-01-24 11:26:30,966] [INFO] Target genome list was writen to GCF_000771285.1_DSM-20211_genomic.fna/target_genomes.txt
[2024-01-24 11:26:30,985] [INFO] Task started: fastANI
[2024-01-24 11:26:30,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgc662708e-68e1-4e80-888d-14e1d1a65aea/GCF_000771285.1_DSM-20211_genomic.fna.gz --refList GCF_000771285.1_DSM-20211_genomic.fna/target_genomes.txt --output GCF_000771285.1_DSM-20211_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:38,590] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:38,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:38,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:38,607] [INFO] Found 15 fastANI hits (10 hits with ANI > threshold)
[2024-01-24 11:26:38,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:38,607] [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. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	100.0	751	752	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	98.8635	647	752	95	conclusive
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	98.8193	652	752	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	96.4387	606	752	95	conclusive
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	96.4386	606	752	95	conclusive
Bifidobacterium longum subsp. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	96.4111	609	752	95	conclusive
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	96.3185	610	752	95	conclusive
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	95.563	577	752	95	conclusive
Bifidobacterium longum subsp. infantis	strain=JCM 1222	GCA_000269965.1	1682	216816	type	True	95.5271	598	752	95	conclusive
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	95.4554	603	752	95	conclusive
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	84.348	512	752	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.4928	410	752	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.8464	234	752	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.3347	61	752	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.2549	53	752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:38,609] [INFO] DFAST Taxonomy check result was written to GCF_000771285.1_DSM-20211_genomic.fna/tc_result.tsv
[2024-01-24 11:26:38,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:38,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:38,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference/checkm_data
[2024-01-24 11:26:38,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:38,635] [INFO] Task started: CheckM
[2024-01-24 11:26:38,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771285.1_DSM-20211_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771285.1_DSM-20211_genomic.fna/checkm_input GCF_000771285.1_DSM-20211_genomic.fna/checkm_result
[2024-01-24 11:27:06,842] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:06,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:06,866] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:06,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:06,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771285.1_DSM-20211_genomic.fna/markers.fasta)
[2024-01-24 11:27:06,868] [INFO] Task started: Blastn
[2024-01-24 11:27:06,868] [INFO] Running command: blastn -query GCF_000771285.1_DSM-20211_genomic.fna/markers.fasta -db /var/lib/cwl/stgea917cda-e95d-419f-b2e2-f5e8a0a94036/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771285.1_DSM-20211_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:08,262] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:08,266] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:08,267] [INFO] Target genome list was writen to GCF_000771285.1_DSM-20211_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:08,274] [INFO] Task started: fastANI
[2024-01-24 11:27:08,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgc662708e-68e1-4e80-888d-14e1d1a65aea/GCF_000771285.1_DSM-20211_genomic.fna.gz --refList GCF_000771285.1_DSM-20211_genomic.fna/target_genomes_gtdb.txt --output GCF_000771285.1_DSM-20211_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:12,724] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:12,737] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:27:12,737] [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	96.4387	606	752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	inconclusive
GCF_000269965.1	s__Bifidobacterium infantis	95.5271	598	752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	inconclusive
GCF_001025175.1	s__Bifidobacterium breve	87.6628	530	752	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	84.4826	514	752	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	84.1191	516	752	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	83.5056	483	752	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	81.5671	408	752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:12,739] [INFO] GTDB search result was written to GCF_000771285.1_DSM-20211_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:12,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:12,743] [INFO] DFAST_QC result json was written to GCF_000771285.1_DSM-20211_genomic.fna/dqc_result.json
[2024-01-24 11:27:12,744] [INFO] DFAST_QC completed!
[2024-01-24 11:27:12,744] [INFO] Total running time: 0h0m52s