[2024-01-24 15:19:04,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference
[2024-01-24 15:19:05,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,623] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,623] [INFO] Running command: gunzip -c /var/lib/cwl/stgc435a165-5b7a-4f26-afe8-042852612d19/GCF_014898155.1_ASM1489815v1_genomic.fna.gz | prodigal -d GCF_014898155.1_ASM1489815v1_genomic.fna/cds.fna -a GCF_014898155.1_ASM1489815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:15,507] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:15,508] [INFO] Task started: HMMsearch
[2024-01-24 15:19:15,508] [INFO] Running command: hmmsearch --tblout GCF_014898155.1_ASM1489815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference/reference_markers.hmm GCF_014898155.1_ASM1489815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:15,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:15,767] [INFO] Found 6/6 markers.
[2024-01-24 15:19:15,795] [INFO] Query marker FASTA was written to GCF_014898155.1_ASM1489815v1_genomic.fna/markers.fasta
[2024-01-24 15:19:15,796] [INFO] Task started: Blastn
[2024-01-24 15:19:15,796] [INFO] Running command: blastn -query GCF_014898155.1_ASM1489815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference/reference_markers.fasta -out GCF_014898155.1_ASM1489815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:16,798] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:16,801] [INFO] Selected 10 target genomes.
[2024-01-24 15:19:16,802] [INFO] Target genome list was writen to GCF_014898155.1_ASM1489815v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:16,809] [INFO] Task started: fastANI
[2024-01-24 15:19:16,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgc435a165-5b7a-4f26-afe8-042852612d19/GCF_014898155.1_ASM1489815v1_genomic.fna.gz --refList GCF_014898155.1_ASM1489815v1_genomic.fna/target_genomes.txt --output GCF_014898155.1_ASM1489815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:23,407] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:23,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:23,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:23,419] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:23,419] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:23,419] [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 eulemuris	strain=DSM 100216	GCA_014898155.1	1765219	1765219	type	True	100.0	971	973	95	conclusive
Bifidobacterium eulemuris	strain=DSM 100216	GCA_002259685.1	1765219	1765219	type	True	99.9893	949	973	95	conclusive
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	93.6798	748	973	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_014898175.1	1603886	1603886	type	True	93.6158	757	973	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	93.5591	745	973	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.2012	479	973	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.7662	460	973	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.8368	288	973	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	77.0838	95	973	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	76.1033	91	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:23,421] [INFO] DFAST Taxonomy check result was written to GCF_014898155.1_ASM1489815v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:23,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:23,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:23,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference/checkm_data
[2024-01-24 15:19:23,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:23,452] [INFO] Task started: CheckM
[2024-01-24 15:19:23,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014898155.1_ASM1489815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014898155.1_ASM1489815v1_genomic.fna/checkm_input GCF_014898155.1_ASM1489815v1_genomic.fna/checkm_result
[2024-01-24 15:19:58,027] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:58,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:58,048] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:58,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:58,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014898155.1_ASM1489815v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:58,049] [INFO] Task started: Blastn
[2024-01-24 15:19:58,049] [INFO] Running command: blastn -query GCF_014898155.1_ASM1489815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd068ebdc-1669-40ad-8154-bcd519616aa9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014898155.1_ASM1489815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:59,548] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:59,551] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:59,551] [INFO] Target genome list was writen to GCF_014898155.1_ASM1489815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:59,561] [INFO] Task started: fastANI
[2024-01-24 15:19:59,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgc435a165-5b7a-4f26-afe8-042852612d19/GCF_014898155.1_ASM1489815v1_genomic.fna.gz --refList GCF_014898155.1_ASM1489815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014898155.1_ASM1489815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:07,526] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:07,541] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:07,541] [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_014898155.1	s__Bifidobacterium eulemuris	100.0	971	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014898175.1	s__Bifidobacterium lemurum	93.6298	758	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.3426	441	973	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	82.2892	427	973	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	82.2309	470	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_002860365.1	s__Bifidobacterium parmae	82.1302	444	973	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	81.9881	480	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_001417815.1	s__Bifidobacterium aesculapii	81.9704	409	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.9507	452	973	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	81.8473	420	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299475.1	s__Bifidobacterium avesanii	81.7149	407	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	81.6204	377	973	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	81.1853	453	973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:07,543] [INFO] GTDB search result was written to GCF_014898155.1_ASM1489815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:07,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:07,547] [INFO] DFAST_QC result json was written to GCF_014898155.1_ASM1489815v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:07,547] [INFO] DFAST_QC completed!
[2024-01-24 15:20:07,547] [INFO] Total running time: 0h1m3s