[2024-01-24 14:40:01,399] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:01,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:01,401] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference
[2024-01-24 14:40:02,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:02,844] [INFO] Task started: Prodigal
[2024-01-24 14:40:02,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bd1f82c-0e4d-4652-bd05-621a4af451da/GCF_014898175.1_ASM1489817v1_genomic.fna.gz | prodigal -d GCF_014898175.1_ASM1489817v1_genomic.fna/cds.fna -a GCF_014898175.1_ASM1489817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:13,672] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:13,672] [INFO] Task started: HMMsearch
[2024-01-24 14:40:13,672] [INFO] Running command: hmmsearch --tblout GCF_014898175.1_ASM1489817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference/reference_markers.hmm GCF_014898175.1_ASM1489817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:13,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:13,948] [INFO] Found 6/6 markers.
[2024-01-24 14:40:13,974] [INFO] Query marker FASTA was written to GCF_014898175.1_ASM1489817v1_genomic.fna/markers.fasta
[2024-01-24 14:40:13,975] [INFO] Task started: Blastn
[2024-01-24 14:40:13,975] [INFO] Running command: blastn -query GCF_014898175.1_ASM1489817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference/reference_markers.fasta -out GCF_014898175.1_ASM1489817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:15,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:15,217] [INFO] Selected 10 target genomes.
[2024-01-24 14:40:15,217] [INFO] Target genome list was writen to GCF_014898175.1_ASM1489817v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:15,226] [INFO] Task started: fastANI
[2024-01-24 14:40:15,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd1f82c-0e4d-4652-bd05-621a4af451da/GCF_014898175.1_ASM1489817v1_genomic.fna.gz --refList GCF_014898175.1_ASM1489817v1_genomic.fna/target_genomes.txt --output GCF_014898175.1_ASM1489817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:22,862] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:22,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:22,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:22,875] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:40:22,875] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:22,876] [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 lemurum	strain=DSM 28807	GCA_014898175.1	1603886	1603886	type	True	100.0	985	988	95	conclusive
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	99.984	958	988	95	conclusive
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	99.9706	939	988	95	conclusive
Bifidobacterium eulemuris	strain=DSM 100216	GCA_014898155.1	1765219	1765219	type	True	93.6645	759	988	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_002259685.1	1765219	1765219	type	True	93.547	755	988	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.23	491	988	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.0136	459	988	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.6936	291	988	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	76.7007	81	988	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	76.383	74	988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:22,877] [INFO] DFAST Taxonomy check result was written to GCF_014898175.1_ASM1489817v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:22,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:22,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:22,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference/checkm_data
[2024-01-24 14:40:22,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:22,910] [INFO] Task started: CheckM
[2024-01-24 14:40:22,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014898175.1_ASM1489817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014898175.1_ASM1489817v1_genomic.fna/checkm_input GCF_014898175.1_ASM1489817v1_genomic.fna/checkm_result
[2024-01-24 14:40:58,802] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:58,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:58,824] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:58,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:58,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014898175.1_ASM1489817v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:58,825] [INFO] Task started: Blastn
[2024-01-24 14:40:58,825] [INFO] Running command: blastn -query GCF_014898175.1_ASM1489817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b17554-8497-4f3a-b14d-e214b5f1a558/dqc_reference/reference_markers_gtdb.fasta -out GCF_014898175.1_ASM1489817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:00,543] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:00,547] [INFO] Selected 16 target genomes.
[2024-01-24 14:41:00,547] [INFO] Target genome list was writen to GCF_014898175.1_ASM1489817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:00,558] [INFO] Task started: fastANI
[2024-01-24 14:41:00,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd1f82c-0e4d-4652-bd05-621a4af451da/GCF_014898175.1_ASM1489817v1_genomic.fna.gz --refList GCF_014898175.1_ASM1489817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014898175.1_ASM1489817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:10,325] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:10,338] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:10,339] [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_014898175.1	s__Bifidobacterium lemurum	100.0	985	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_014898155.1	s__Bifidobacterium eulemuris	93.6606	760	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.6167	446	988	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	82.4961	452	988	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	82.3931	457	988	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	82.3732	479	988	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	82.2785	444	988	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	82.2448	471	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_000741175.1	s__Bifidobacterium callitrichos	82.1064	441	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_018555635.1	s__Bifidobacterium sp018555635	82.0508	439	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	82.043	454	988	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	82.0377	444	988	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	82.0117	463	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	81.9459	423	988	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	81.6289	405	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	79.7685	295	988	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:10,341] [INFO] GTDB search result was written to GCF_014898175.1_ASM1489817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:10,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:10,345] [INFO] DFAST_QC result json was written to GCF_014898175.1_ASM1489817v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:10,345] [INFO] DFAST_QC completed!
[2024-01-24 14:41:10,345] [INFO] Total running time: 0h1m9s