[2023-06-28 11:30:30,261] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:30:30,267] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:30:30,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference
[2023-06-28 11:30:31,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:30:31,453] [INFO] Task started: Prodigal
[2023-06-28 11:30:31,453] [INFO] Running command: gunzip -c /var/lib/cwl/stg6802568f-4ef4-4eff-a293-294fe1dec0ef/GCA_944320175.1_BRZ_MH_bin54_genomic.fna.gz | prodigal -d GCA_944320175.1_BRZ_MH_bin54_genomic.fna/cds.fna -a GCA_944320175.1_BRZ_MH_bin54_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:30:36,372] [INFO] Task succeeded: Prodigal
[2023-06-28 11:30:36,372] [INFO] Task started: HMMsearch
[2023-06-28 11:30:36,372] [INFO] Running command: hmmsearch --tblout GCA_944320175.1_BRZ_MH_bin54_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference/reference_markers.hmm GCA_944320175.1_BRZ_MH_bin54_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:30:36,548] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:30:36,549] [INFO] Found 6/6 markers.
[2023-06-28 11:30:36,567] [INFO] Query marker FASTA was written to GCA_944320175.1_BRZ_MH_bin54_genomic.fna/markers.fasta
[2023-06-28 11:30:36,567] [INFO] Task started: Blastn
[2023-06-28 11:30:36,568] [INFO] Running command: blastn -query GCA_944320175.1_BRZ_MH_bin54_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference/reference_markers.fasta -out GCA_944320175.1_BRZ_MH_bin54_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:30:37,489] [INFO] Task succeeded: Blastn
[2023-06-28 11:30:37,492] [INFO] Selected 12 target genomes.
[2023-06-28 11:30:37,492] [INFO] Target genome list was writen to GCA_944320175.1_BRZ_MH_bin54_genomic.fna/target_genomes.txt
[2023-06-28 11:30:37,494] [INFO] Task started: fastANI
[2023-06-28 11:30:37,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg6802568f-4ef4-4eff-a293-294fe1dec0ef/GCA_944320175.1_BRZ_MH_bin54_genomic.fna.gz --refList GCA_944320175.1_BRZ_MH_bin54_genomic.fna/target_genomes.txt --output GCA_944320175.1_BRZ_MH_bin54_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:30:43,491] [INFO] Task succeeded: fastANI
[2023-06-28 11:30:43,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:30:43,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:30:43,502] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:30:43,502] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:30:43,502] [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 pullorum subsp. gallinarum	strain=LMG 11586	GCA_000741215.1	78344	78448	type	True	90.6938	449	509	95	below_threshold
Bifidobacterium pullorum subsp. gallinarum	strain=DSM 20670	GCA_000771505.1	78344	78448	type	True	90.6839	442	509	95	below_threshold
Bifidobacterium pullorum subsp. saeculare	strain=DSM 6531	GCA_000770965.1	78257	78448	type	True	90.6797	436	509	95	below_threshold
Bifidobacterium pullorum subsp. saeculare	strain=LMG 14934	GCA_000741375.1	78257	78448	type	True	90.6074	458	509	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	84.7699	418	509	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	82.3359	320	509	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	82.2605	339	509	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.0501	326	509	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.8475	312	509	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.1195	234	509	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5213	79	509	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	75.9063	84	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:30:43,504] [INFO] DFAST Taxonomy check result was written to GCA_944320175.1_BRZ_MH_bin54_genomic.fna/tc_result.tsv
[2023-06-28 11:30:43,504] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:30:43,505] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:30:43,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference/checkm_data
[2023-06-28 11:30:43,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:30:43,525] [INFO] Task started: CheckM
[2023-06-28 11:30:43,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320175.1_BRZ_MH_bin54_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320175.1_BRZ_MH_bin54_genomic.fna/checkm_input GCA_944320175.1_BRZ_MH_bin54_genomic.fna/checkm_result
[2023-06-28 11:31:04,007] [INFO] Task succeeded: CheckM
[2023-06-28 11:31:04,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:31:04,024] [INFO] ===== Completeness check finished =====
[2023-06-28 11:31:04,025] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:31:04,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320175.1_BRZ_MH_bin54_genomic.fna/markers.fasta)
[2023-06-28 11:31:04,025] [INFO] Task started: Blastn
[2023-06-28 11:31:04,025] [INFO] Running command: blastn -query GCA_944320175.1_BRZ_MH_bin54_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab6ae23-fb8b-4b4f-ad5e-744960e00cce/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320175.1_BRZ_MH_bin54_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:31:05,400] [INFO] Task succeeded: Blastn
[2023-06-28 11:31:05,404] [INFO] Selected 17 target genomes.
[2023-06-28 11:31:05,404] [INFO] Target genome list was writen to GCA_944320175.1_BRZ_MH_bin54_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:31:05,411] [INFO] Task started: fastANI
[2023-06-28 11:31:05,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg6802568f-4ef4-4eff-a293-294fe1dec0ef/GCA_944320175.1_BRZ_MH_bin54_genomic.fna.gz --refList GCA_944320175.1_BRZ_MH_bin54_genomic.fna/target_genomes_gtdb.txt --output GCA_944320175.1_BRZ_MH_bin54_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:31:14,576] [INFO] Task succeeded: fastANI
[2023-06-28 11:31:14,590] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:31:14,591] [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_000771405.1	s__Bifidobacterium pullorum	97.7521	475	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	conclusive
GCF_000741215.1	s__Bifidobacterium pullorum_B	90.7301	448	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_016899725.1	s__Bifidobacterium pullorum_C	82.655	314	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	82.3117	321	509	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	82.1936	352	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.057	316	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898155.1	s__Bifidobacterium eulemuris	82.0077	317	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002860365.1	s__Bifidobacterium parmae	81.9131	305	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	81.8005	291	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698235.1	s__Bifidobacterium rousetti	81.7527	320	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.7406	306	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	81.6823	300	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932675.1	s__Bifidobacterium sp012932675	81.0148	269	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000522505.1	s__Bifidobacterium moukalabense	80.6774	266	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_000967185.1	s__Bifidobacterium asteroides_B	78.5743	144	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_000499285.1	s__Bifidobacterium sp000499285	78.3914	133	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202755.1	s__Bifidobacterium asteroides_F	77.9424	124	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:31:14,593] [INFO] GTDB search result was written to GCA_944320175.1_BRZ_MH_bin54_genomic.fna/result_gtdb.tsv
[2023-06-28 11:31:14,594] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:31:14,598] [INFO] DFAST_QC result json was written to GCA_944320175.1_BRZ_MH_bin54_genomic.fna/dqc_result.json
[2023-06-28 11:31:14,598] [INFO] DFAST_QC completed!
[2023-06-28 11:31:14,598] [INFO] Total running time: 0h0m44s