[2023-06-12 23:27:53,411] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:27:53,414] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:27:53,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference
[2023-06-12 23:27:54,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:27:54,913] [INFO] Task started: Prodigal
[2023-06-12 23:27:54,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg4409099b-92af-4b95-9fca-7addd538d8d6/GCA_022721075.1_ASM2272107v1_genomic.fna.gz | prodigal -d GCA_022721075.1_ASM2272107v1_genomic.fna/cds.fna -a GCA_022721075.1_ASM2272107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:28:02,172] [INFO] Task succeeded: Prodigal
[2023-06-12 23:28:02,173] [INFO] Task started: HMMsearch
[2023-06-12 23:28:02,173] [INFO] Running command: hmmsearch --tblout GCA_022721075.1_ASM2272107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference/reference_markers.hmm GCA_022721075.1_ASM2272107v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:28:02,428] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:28:02,429] [INFO] Found 6/6 markers.
[2023-06-12 23:28:02,453] [INFO] Query marker FASTA was written to GCA_022721075.1_ASM2272107v1_genomic.fna/markers.fasta
[2023-06-12 23:28:02,453] [INFO] Task started: Blastn
[2023-06-12 23:28:02,453] [INFO] Running command: blastn -query GCA_022721075.1_ASM2272107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference/reference_markers.fasta -out GCA_022721075.1_ASM2272107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:28:03,471] [INFO] Task succeeded: Blastn
[2023-06-12 23:28:03,475] [INFO] Selected 15 target genomes.
[2023-06-12 23:28:03,476] [INFO] Target genome list was writen to GCA_022721075.1_ASM2272107v1_genomic.fna/target_genomes.txt
[2023-06-12 23:28:03,477] [INFO] Task started: fastANI
[2023-06-12 23:28:03,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg4409099b-92af-4b95-9fca-7addd538d8d6/GCA_022721075.1_ASM2272107v1_genomic.fna.gz --refList GCA_022721075.1_ASM2272107v1_genomic.fna/target_genomes.txt --output GCA_022721075.1_ASM2272107v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:28:10,896] [INFO] Task succeeded: fastANI
[2023-06-12 23:28:10,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:28:10,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:28:10,912] [INFO] Found 15 fastANI hits (5 hits with ANI > threshold)
[2023-06-12 23:28:10,913] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-12 23:28:10,913] [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 bifidum	strain=JCM 1255	GCA_001025135.1	1681	1681	type	True	99.0758	637	699	95	conclusive
Bifidobacterium bifidum	strain=NCTC13001	GCA_900637095.1	1681	1681	type	True	99.0747	636	699	95	conclusive
Bifidobacterium bifidum	strain=DSM 20456	GCA_000771485.1	1681	1681	type	True	99.0597	625	699	95	conclusive
Bifidobacterium bifidum	strain=LMG 11041	GCA_000741085.1	1681	1681	type	True	99.0399	641	699	95	conclusive
Bifidobacterium bifidum	strain=ATCC 29521	GCA_000466525.1	1681	1681	type	True	99.0192	634	699	95	conclusive
Bifidobacterium longum subsp. longum	strain=LMG 13197	GCA_000741245.1	1679	216816	type	True	82.8064	353	699	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	82.7534	356	699	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	82.7339	356	699	95	below_threshold
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	82.725	357	699	95	below_threshold
Bifidobacterium longum subsp. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	82.6463	362	699	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.2583	387	699	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.6265	369	699	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.3171	244	699	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.0889	122	699	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.5235	77	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:28:10,917] [INFO] DFAST Taxonomy check result was written to GCA_022721075.1_ASM2272107v1_genomic.fna/tc_result.tsv
[2023-06-12 23:28:10,917] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:28:10,918] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:28:10,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference/checkm_data
[2023-06-12 23:28:10,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:28:10,952] [INFO] Task started: CheckM
[2023-06-12 23:28:10,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022721075.1_ASM2272107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022721075.1_ASM2272107v1_genomic.fna/checkm_input GCA_022721075.1_ASM2272107v1_genomic.fna/checkm_result
[2023-06-12 23:28:38,819] [INFO] Task succeeded: CheckM
[2023-06-12 23:28:38,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-12 23:28:38,847] [INFO] ===== Completeness check finished =====
[2023-06-12 23:28:38,848] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:28:38,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022721075.1_ASM2272107v1_genomic.fna/markers.fasta)
[2023-06-12 23:28:38,849] [INFO] Task started: Blastn
[2023-06-12 23:28:38,849] [INFO] Running command: blastn -query GCA_022721075.1_ASM2272107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51bb3b68-be02-44ba-9a62-30734b37723c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022721075.1_ASM2272107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:28:40,301] [INFO] Task succeeded: Blastn
[2023-06-12 23:28:40,306] [INFO] Selected 22 target genomes.
[2023-06-12 23:28:40,306] [INFO] Target genome list was writen to GCA_022721075.1_ASM2272107v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:28:40,309] [INFO] Task started: fastANI
[2023-06-12 23:28:40,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg4409099b-92af-4b95-9fca-7addd538d8d6/GCA_022721075.1_ASM2272107v1_genomic.fna.gz --refList GCA_022721075.1_ASM2272107v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022721075.1_ASM2272107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:28:51,450] [INFO] Task succeeded: fastANI
[2023-06-12 23:28:51,473] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:28:51,474] [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_001025135.1	s__Bifidobacterium bifidum	99.0758	637	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	conclusive
GCF_009193355.1	s__Bifidobacterium leontopitheci	83.1248	472	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196555.1	s__Bifidobacterium longum	82.737	357	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_010667685.1	s__Bifidobacterium aerophilum	82.3083	396	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	82.1686	432	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_018555385.1	s__Bifidobacterium sp018555385	82.1233	388	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.081	387	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	82.0717	375	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	82.047	372	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009299505.1	s__Bifidobacterium ramosum	82.0203	414	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008698235.1	s__Bifidobacterium rousetti	81.9995	389	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_018555335.1	s__Bifidobacterium sp018555335	81.9126	378	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	81.875	376	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000269965.1	s__Bifidobacterium infantis	81.8565	360	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_003952945.1	s__Bifidobacterium samirii	81.8246	369	699	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	81.6908	360	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_001025175.1	s__Bifidobacterium breve	81.5052	329	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.3631	365	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009078285.1	s__Bifidobacterium jacchi	81.3363	399	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771405.1	s__Bifidobacterium pullorum	80.9588	312	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003951095.1	s__Bifidobacterium goeldii	80.1032	282	699	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:28:51,476] [INFO] GTDB search result was written to GCA_022721075.1_ASM2272107v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:28:51,477] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:28:51,482] [INFO] DFAST_QC result json was written to GCA_022721075.1_ASM2272107v1_genomic.fna/dqc_result.json
[2023-06-12 23:28:51,482] [INFO] DFAST_QC completed!
[2023-06-12 23:28:51,482] [INFO] Total running time: 0h0m58s