[2024-01-24 13:40:45,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference
[2024-01-24 13:40:47,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,126] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg42286195-cbec-478e-ac86-88c99399984d/GCF_900637145.1_49569_E01_genomic.fna.gz | prodigal -d GCF_900637145.1_49569_E01_genomic.fna/cds.fna -a GCF_900637145.1_49569_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:55,144] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:55,145] [INFO] Task started: HMMsearch
[2024-01-24 13:40:55,145] [INFO] Running command: hmmsearch --tblout GCF_900637145.1_49569_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference/reference_markers.hmm GCF_900637145.1_49569_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:55,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:55,383] [INFO] Found 6/6 markers.
[2024-01-24 13:40:55,403] [INFO] Query marker FASTA was written to GCF_900637145.1_49569_E01_genomic.fna/markers.fasta
[2024-01-24 13:40:55,404] [INFO] Task started: Blastn
[2024-01-24 13:40:55,404] [INFO] Running command: blastn -query GCF_900637145.1_49569_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference/reference_markers.fasta -out GCF_900637145.1_49569_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,254] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,258] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:56,259] [INFO] Target genome list was writen to GCF_900637145.1_49569_E01_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,294] [INFO] Task started: fastANI
[2024-01-24 13:40:56,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg42286195-cbec-478e-ac86-88c99399984d/GCF_900637145.1_49569_E01_genomic.fna.gz --refList GCF_900637145.1_49569_E01_genomic.fna/target_genomes.txt --output GCF_900637145.1_49569_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:03,023] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:03,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:03,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:03,035] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:41:03,035] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:03,035] [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	100.0	757	758	95	conclusive
Bifidobacterium breve	strain=JCM 1192	GCA_001025175.1	1685	1685	type	True	99.9952	756	758	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000158015.1	1685	1685	type	True	99.9842	752	758	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000771305.1	1685	1685	type	True	99.9748	735	758	95	conclusive
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	87.5944	524	758	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	87.572	515	758	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	86.9368	524	758	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.2249	481	758	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	82.8888	459	758	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.2423	357	758	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.7953	210	758	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.7879	132	758	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.151	56	758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:03,037] [INFO] DFAST Taxonomy check result was written to GCF_900637145.1_49569_E01_genomic.fna/tc_result.tsv
[2024-01-24 13:41:03,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:03,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:03,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference/checkm_data
[2024-01-24 13:41:03,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:03,071] [INFO] Task started: CheckM
[2024-01-24 13:41:03,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637145.1_49569_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637145.1_49569_E01_genomic.fna/checkm_input GCF_900637145.1_49569_E01_genomic.fna/checkm_result
[2024-01-24 13:41:31,932] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:31,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,957] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:31,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:31,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637145.1_49569_E01_genomic.fna/markers.fasta)
[2024-01-24 13:41:31,958] [INFO] Task started: Blastn
[2024-01-24 13:41:31,959] [INFO] Running command: blastn -query GCF_900637145.1_49569_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbf90b5-258b-4c63-a961-5d6d1a250730/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637145.1_49569_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:33,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:33,148] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:33,149] [INFO] Target genome list was writen to GCF_900637145.1_49569_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:33,370] [INFO] Task started: fastANI
[2024-01-24 13:41:33,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg42286195-cbec-478e-ac86-88c99399984d/GCF_900637145.1_49569_E01_genomic.fna.gz --refList GCF_900637145.1_49569_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637145.1_49569_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:39,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:39,873] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:39,873] [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	99.9952	756	758	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	87.6163	560	758	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	86.8901	527	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_018555355.1	s__Bifidobacterium sp018555355	83.2067	483	758	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	83.2057	470	758	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	82.8987	459	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_000741695.1	s__Bifidobacterium reuteri	82.8504	434	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_009193305.1	s__Bifidobacterium cebidarum	82.6922	427	758	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	82.4953	437	758	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	82.2912	420	758	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	81.199	377	758	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 13:41:39,875] [INFO] GTDB search result was written to GCF_900637145.1_49569_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:39,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:39,879] [INFO] DFAST_QC result json was written to GCF_900637145.1_49569_E01_genomic.fna/dqc_result.json
[2024-01-24 13:41:39,879] [INFO] DFAST_QC completed!
[2024-01-24 13:41:39,879] [INFO] Total running time: 0h0m54s