[2024-01-24 13:12:37,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:37,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:37,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference
[2024-01-24 13:12:38,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:38,550] [INFO] Task started: Prodigal
[2024-01-24 13:12:38,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg0733fc44-9d92-4532-a8fb-e3af834abec1/GCF_001005065.1_ASM100506v1_genomic.fna.gz | prodigal -d GCF_001005065.1_ASM100506v1_genomic.fna/cds.fna -a GCF_001005065.1_ASM100506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:48,338] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:48,338] [INFO] Task started: HMMsearch
[2024-01-24 13:12:48,338] [INFO] Running command: hmmsearch --tblout GCF_001005065.1_ASM100506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference/reference_markers.hmm GCF_001005065.1_ASM100506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:48,673] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:48,674] [INFO] Found 6/6 markers.
[2024-01-24 13:12:48,707] [INFO] Query marker FASTA was written to GCF_001005065.1_ASM100506v1_genomic.fna/markers.fasta
[2024-01-24 13:12:48,707] [INFO] Task started: Blastn
[2024-01-24 13:12:48,707] [INFO] Running command: blastn -query GCF_001005065.1_ASM100506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference/reference_markers.fasta -out GCF_001005065.1_ASM100506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:49,926] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:49,930] [INFO] Selected 14 target genomes.
[2024-01-24 13:12:49,930] [INFO] Target genome list was writen to GCF_001005065.1_ASM100506v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:49,949] [INFO] Task started: fastANI
[2024-01-24 13:12:49,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg0733fc44-9d92-4532-a8fb-e3af834abec1/GCF_001005065.1_ASM100506v1_genomic.fna.gz --refList GCF_001005065.1_ASM100506v1_genomic.fna/target_genomes.txt --output GCF_001005065.1_ASM100506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:59,426] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:59,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:59,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:59,442] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:12:59,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:59,442] [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 scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	100.0	1025	1027	95	conclusive
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	99.9998	1026	1027	95	conclusive
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	99.9111	971	1027	95	conclusive
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	84.1082	563	1027	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	84.0385	584	1027	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	84.03	572	1027	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	83.9437	566	1027	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	83.6389	516	1027	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	83.3577	494	1027	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	82.7798	483	1027	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.4463	509	1027	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.9389	333	1027	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.1146	182	1027	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.4066	148	1027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:59,446] [INFO] DFAST Taxonomy check result was written to GCF_001005065.1_ASM100506v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:59,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:59,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:59,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference/checkm_data
[2024-01-24 13:12:59,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:59,485] [INFO] Task started: CheckM
[2024-01-24 13:12:59,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005065.1_ASM100506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005065.1_ASM100506v1_genomic.fna/checkm_input GCF_001005065.1_ASM100506v1_genomic.fna/checkm_result
[2024-01-24 13:13:33,916] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:33,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:33,934] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:33,935] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:33,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005065.1_ASM100506v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:33,936] [INFO] Task started: Blastn
[2024-01-24 13:13:33,936] [INFO] Running command: blastn -query GCF_001005065.1_ASM100506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg674e88d6-5f15-4407-8b4b-a3671e8d93ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005065.1_ASM100506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:35,665] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:35,668] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:35,669] [INFO] Target genome list was writen to GCF_001005065.1_ASM100506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:35,688] [INFO] Task started: fastANI
[2024-01-24 13:13:35,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg0733fc44-9d92-4532-a8fb-e3af834abec1/GCF_001005065.1_ASM100506v1_genomic.fna.gz --refList GCF_001005065.1_ASM100506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005065.1_ASM100506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:45,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:45,821] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:45,821] [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_001042635.1	s__Bifidobacterium scardovii	99.9998	1026	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	conclusive
GCF_009299505.1	s__Bifidobacterium ramosum	84.0283	573	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667685.1	s__Bifidobacterium aerophilum	83.9499	566	1027	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	83.6288	517	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	83.5937	544	1027	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	83.5926	523	1027	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	83.5207	543	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	83.3667	494	1027	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	82.7983	482	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932365.1	s__Bifidobacterium sp012932365	82.7219	460	1027	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	82.6396	468	1027	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	82.5659	485	1027	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	82.5294	489	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	82.19	422	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_000771405.1	s__Bifidobacterium pullorum	82.1235	413	1027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_014898175.1	s__Bifidobacterium lemurum	82.0786	470	1027	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 13:13:45,823] [INFO] GTDB search result was written to GCF_001005065.1_ASM100506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:45,824] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:45,830] [INFO] DFAST_QC result json was written to GCF_001005065.1_ASM100506v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:45,830] [INFO] DFAST_QC completed!
[2024-01-24 13:13:45,830] [INFO] Total running time: 0h1m9s