[2024-01-24 11:12:39,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference
[2024-01-24 11:12:41,214] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,215] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,215] [INFO] Running command: gunzip -c /var/lib/cwl/stg49512224-3e4d-4d17-a717-bcd7ce0cd396/GCF_000771685.1_DSM-23975_genomic.fna.gz | prodigal -d GCF_000771685.1_DSM-23975_genomic.fna/cds.fna -a GCF_000771685.1_DSM-23975_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,575] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,576] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,576] [INFO] Running command: hmmsearch --tblout GCF_000771685.1_DSM-23975_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference/reference_markers.hmm GCF_000771685.1_DSM-23975_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,831] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,930] [INFO] Query marker FASTA was written to GCF_000771685.1_DSM-23975_genomic.fna/markers.fasta
[2024-01-24 11:12:50,930] [INFO] Task started: Blastn
[2024-01-24 11:12:50,930] [INFO] Running command: blastn -query GCF_000771685.1_DSM-23975_genomic.fna/markers.fasta -db /var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference/reference_markers.fasta -out GCF_000771685.1_DSM-23975_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,781] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,784] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:51,784] [INFO] Target genome list was writen to GCF_000771685.1_DSM-23975_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,790] [INFO] Task started: fastANI
[2024-01-24 11:12:51,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg49512224-3e4d-4d17-a717-bcd7ce0cd396/GCF_000771685.1_DSM-23975_genomic.fna.gz --refList GCF_000771685.1_DSM-23975_genomic.fna/target_genomes.txt --output GCF_000771685.1_DSM-23975_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:01,404] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:01,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:01,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:01,426] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:01,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:01,427] [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 reuteri	strain=DSM 23975	GCA_000771685.1	983706	983706	type	True	100.0	917	919	95	conclusive
Bifidobacterium reuteri	strain=DSM 23975	GCA_000741695.1	983706	983706	type	True	99.9778	910	919	95	conclusive
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	85.5701	597	919	95	below_threshold
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	84.187	551	919	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.8616	544	919	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	83.5579	445	919	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	83.4958	463	919	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	82.9387	463	919	95	below_threshold
Bifidobacterium imperatoris	strain=Tam1G	GCA_002860405.1	2020965	2020965	type	True	82.4646	487	919	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.8065	410	919	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	80.9912	393	919	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	80.9847	394	919	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.7495	240	919	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	76.488	55	919	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:01,429] [INFO] DFAST Taxonomy check result was written to GCF_000771685.1_DSM-23975_genomic.fna/tc_result.tsv
[2024-01-24 11:13:01,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:01,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:01,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference/checkm_data
[2024-01-24 11:13:01,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:01,466] [INFO] Task started: CheckM
[2024-01-24 11:13:01,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771685.1_DSM-23975_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771685.1_DSM-23975_genomic.fna/checkm_input GCF_000771685.1_DSM-23975_genomic.fna/checkm_result
[2024-01-24 11:13:34,200] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:34,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:34,219] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:34,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:34,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771685.1_DSM-23975_genomic.fna/markers.fasta)
[2024-01-24 11:13:34,220] [INFO] Task started: Blastn
[2024-01-24 11:13:34,220] [INFO] Running command: blastn -query GCF_000771685.1_DSM-23975_genomic.fna/markers.fasta -db /var/lib/cwl/stg3660b331-5509-42c9-aa8c-2bdf3dc44f86/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771685.1_DSM-23975_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:35,450] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:35,454] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:35,454] [INFO] Target genome list was writen to GCF_000771685.1_DSM-23975_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:35,465] [INFO] Task started: fastANI
[2024-01-24 11:13:35,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg49512224-3e4d-4d17-a717-bcd7ce0cd396/GCF_000771685.1_DSM-23975_genomic.fna.gz --refList GCF_000771685.1_DSM-23975_genomic.fna/target_genomes_gtdb.txt --output GCF_000771685.1_DSM-23975_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:44,606] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:44,640] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:44,640] [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_000741695.1	s__Bifidobacterium reuteri	99.9778	910	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	conclusive
GCF_002259745.1	s__Bifidobacterium myosotis	85.5709	597	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	84.2045	550	919	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	83.9026	532	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_000269965.1	s__Bifidobacterium infantis	83.5085	462	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_018555455.1	s__Bifidobacterium sp018555455	83.349	507	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193305.1	s__Bifidobacterium cebidarum	83.3239	510	919	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	82.8906	475	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_002802915.1	s__Bifidobacterium felsineum	82.8717	513	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_002860405.1	s__Bifidobacterium imperatoris	82.4646	487	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009299505.1	s__Bifidobacterium ramosum	81.9028	444	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014898155.1	s__Bifidobacterium eulemuris	81.1293	381	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014898175.1	s__Bifidobacterium lemurum	81.0281	398	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:44,642] [INFO] GTDB search result was written to GCF_000771685.1_DSM-23975_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:44,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:44,646] [INFO] DFAST_QC result json was written to GCF_000771685.1_DSM-23975_genomic.fna/dqc_result.json
[2024-01-24 11:13:44,646] [INFO] DFAST_QC completed!
[2024-01-24 11:13:44,646] [INFO] Total running time: 0h1m5s