[2024-01-24 12:45:20,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference
[2024-01-24 12:45:21,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:21,931] [INFO] Task started: Prodigal
[2024-01-24 12:45:21,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg53847b15-9765-4235-bc65-d6ff05773d8d/GCF_002259745.1_ASM225974v1_genomic.fna.gz | prodigal -d GCF_002259745.1_ASM225974v1_genomic.fna/cds.fna -a GCF_002259745.1_ASM225974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:31,648] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:31,649] [INFO] Task started: HMMsearch
[2024-01-24 12:45:31,649] [INFO] Running command: hmmsearch --tblout GCF_002259745.1_ASM225974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference/reference_markers.hmm GCF_002259745.1_ASM225974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:31,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:31,892] [INFO] Found 6/6 markers.
[2024-01-24 12:45:31,926] [INFO] Query marker FASTA was written to GCF_002259745.1_ASM225974v1_genomic.fna/markers.fasta
[2024-01-24 12:45:31,926] [INFO] Task started: Blastn
[2024-01-24 12:45:31,927] [INFO] Running command: blastn -query GCF_002259745.1_ASM225974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference/reference_markers.fasta -out GCF_002259745.1_ASM225974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:32,939] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:32,944] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:32,944] [INFO] Target genome list was writen to GCF_002259745.1_ASM225974v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:32,959] [INFO] Task started: fastANI
[2024-01-24 12:45:32,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg53847b15-9765-4235-bc65-d6ff05773d8d/GCF_002259745.1_ASM225974v1_genomic.fna.gz --refList GCF_002259745.1_ASM225974v1_genomic.fna/target_genomes.txt --output GCF_002259745.1_ASM225974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:41,034] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:41,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:41,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:41,052] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:41,052] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:41,053] [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 myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	100.0	949	952	95	conclusive
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	86.4264	679	952	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	86.1751	683	952	95	below_threshold
Bifidobacterium reuteri	strain=DSM 23975	GCA_000741695.1	983706	983706	type	True	85.9138	593	952	95	below_threshold
Bifidobacterium reuteri	strain=DSM 23975	GCA_000771685.1	983706	983706	type	True	85.7501	584	952	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	83.5306	476	952	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	83.5016	452	952	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	83.4373	483	952	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	83.3991	484	952	95	below_threshold
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	83.3683	480	952	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	83.1875	478	952	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.4464	499	952	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.2734	268	952	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.0956	154	952	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	76.6634	68	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:41,054] [INFO] DFAST Taxonomy check result was written to GCF_002259745.1_ASM225974v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:41,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:41,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:41,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference/checkm_data
[2024-01-24 12:45:41,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:41,092] [INFO] Task started: CheckM
[2024-01-24 12:45:41,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002259745.1_ASM225974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002259745.1_ASM225974v1_genomic.fna/checkm_input GCF_002259745.1_ASM225974v1_genomic.fna/checkm_result
[2024-01-24 12:46:12,991] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:12,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:13,018] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:13,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:13,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002259745.1_ASM225974v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:13,019] [INFO] Task started: Blastn
[2024-01-24 12:46:13,019] [INFO] Running command: blastn -query GCF_002259745.1_ASM225974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg566c9e3a-9bde-445a-b7fd-d360b7daaa01/dqc_reference/reference_markers_gtdb.fasta -out GCF_002259745.1_ASM225974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:14,465] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:14,469] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:14,470] [INFO] Target genome list was writen to GCF_002259745.1_ASM225974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:14,491] [INFO] Task started: fastANI
[2024-01-24 12:46:14,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg53847b15-9765-4235-bc65-d6ff05773d8d/GCF_002259745.1_ASM225974v1_genomic.fna.gz --refList GCF_002259745.1_ASM225974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002259745.1_ASM225974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:19,658] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:19,674] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:19,674] [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_002259745.1	s__Bifidobacterium myosotis	100.0	949	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	conclusive
GCF_003129905.1	s__Bifidobacterium callitrichidarum	86.4437	678	952	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	86.4291	640	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_000741695.1	s__Bifidobacterium reuteri	85.898	594	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_000269965.1	s__Bifidobacterium infantis	83.5356	473	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_000196555.1	s__Bifidobacterium longum	83.4361	480	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_001025175.1	s__Bifidobacterium breve	82.9705	444	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_018555455.1	s__Bifidobacterium sp018555455	82.8286	497	952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:19,677] [INFO] GTDB search result was written to GCF_002259745.1_ASM225974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:19,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:19,682] [INFO] DFAST_QC result json was written to GCF_002259745.1_ASM225974v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:19,683] [INFO] DFAST_QC completed!
[2024-01-24 12:46:19,683] [INFO] Total running time: 0h0m59s