[2023-06-13 10:35:40,960] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:35:40,963] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:35:40,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference
[2023-06-13 10:35:43,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:35:43,352] [INFO] Task started: Prodigal
[2023-06-13 10:35:43,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f18ba1a-002b-456b-9bf2-1b8c813355ce/GCA_022744625.1_ASM2274462v1_genomic.fna.gz | prodigal -d GCA_022744625.1_ASM2274462v1_genomic.fna/cds.fna -a GCA_022744625.1_ASM2274462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:35:50,692] [INFO] Task succeeded: Prodigal
[2023-06-13 10:35:50,693] [INFO] Task started: HMMsearch
[2023-06-13 10:35:50,693] [INFO] Running command: hmmsearch --tblout GCA_022744625.1_ASM2274462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference/reference_markers.hmm GCA_022744625.1_ASM2274462v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:35:50,961] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:35:50,963] [INFO] Found 6/6 markers.
[2023-06-13 10:35:50,987] [INFO] Query marker FASTA was written to GCA_022744625.1_ASM2274462v1_genomic.fna/markers.fasta
[2023-06-13 10:35:50,988] [INFO] Task started: Blastn
[2023-06-13 10:35:50,988] [INFO] Running command: blastn -query GCA_022744625.1_ASM2274462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference/reference_markers.fasta -out GCA_022744625.1_ASM2274462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:35:51,842] [INFO] Task succeeded: Blastn
[2023-06-13 10:35:51,847] [INFO] Selected 12 target genomes.
[2023-06-13 10:35:51,848] [INFO] Target genome list was writen to GCA_022744625.1_ASM2274462v1_genomic.fna/target_genomes.txt
[2023-06-13 10:35:51,852] [INFO] Task started: fastANI
[2023-06-13 10:35:51,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f18ba1a-002b-456b-9bf2-1b8c813355ce/GCA_022744625.1_ASM2274462v1_genomic.fna.gz --refList GCA_022744625.1_ASM2274462v1_genomic.fna/target_genomes.txt --output GCA_022744625.1_ASM2274462v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:35:57,923] [INFO] Task succeeded: fastANI
[2023-06-13 10:35:57,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:35:57,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:35:57,940] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 10:35:57,944] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 10:35:57,945] [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 breve	strain=DSM 20213	GCA_000771305.1	1685	1685	type	True	98.4855	589	682	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000158015.1	1685	1685	type	True	98.343	598	682	95	conclusive
Bifidobacterium breve	strain=NCTC11815	GCA_900637145.1	1685	1685	type	True	98.2057	605	682	95	conclusive
Bifidobacterium breve	strain=JCM 1192	GCA_001025175.1	1685	1685	type	True	98.2024	606	682	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	86.4632	454	682	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	86.3715	444	682	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.9336	431	682	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	82.4862	405	682	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.8405	315	682	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.4367	180	682	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.4383	104	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:35:57,948] [INFO] DFAST Taxonomy check result was written to GCA_022744625.1_ASM2274462v1_genomic.fna/tc_result.tsv
[2023-06-13 10:35:57,948] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:35:57,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:35:57,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference/checkm_data
[2023-06-13 10:35:57,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:35:57,985] [INFO] Task started: CheckM
[2023-06-13 10:35:57,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744625.1_ASM2274462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744625.1_ASM2274462v1_genomic.fna/checkm_input GCA_022744625.1_ASM2274462v1_genomic.fna/checkm_result
[2023-06-13 10:36:25,281] [INFO] Task succeeded: CheckM
[2023-06-13 10:36:25,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 10:36:25,305] [INFO] ===== Completeness check finished =====
[2023-06-13 10:36:25,306] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:36:25,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744625.1_ASM2274462v1_genomic.fna/markers.fasta)
[2023-06-13 10:36:25,306] [INFO] Task started: Blastn
[2023-06-13 10:36:25,307] [INFO] Running command: blastn -query GCA_022744625.1_ASM2274462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b4fc76d-6b89-4904-b415-d62f03ab9744/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744625.1_ASM2274462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:36:26,512] [INFO] Task succeeded: Blastn
[2023-06-13 10:36:26,518] [INFO] Selected 12 target genomes.
[2023-06-13 10:36:26,518] [INFO] Target genome list was writen to GCA_022744625.1_ASM2274462v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:36:26,524] [INFO] Task started: fastANI
[2023-06-13 10:36:26,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f18ba1a-002b-456b-9bf2-1b8c813355ce/GCA_022744625.1_ASM2274462v1_genomic.fna.gz --refList GCA_022744625.1_ASM2274462v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744625.1_ASM2274462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:36:33,055] [INFO] Task succeeded: fastANI
[2023-06-13 10:36:33,071] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:36:33,071] [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_001025175.1	s__Bifidobacterium breve	98.1933	606	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	conclusive
GCF_000269965.1	s__Bifidobacterium infantis	86.4433	469	682	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	86.3715	444	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	82.9057	424	682	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	82.8792	431	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_002259745.1	s__Bifidobacterium myosotis	82.4745	404	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_000741695.1	s__Bifidobacterium reuteri	82.3909	407	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_018555455.1	s__Bifidobacterium sp018555455	82.3466	379	682	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	82.2421	382	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932375.1	s__Bifidobacterium sp012932375	81.8594	376	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932425.1	s__Bifidobacterium sp012932425	80.7362	344	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:36:33,074] [INFO] GTDB search result was written to GCA_022744625.1_ASM2274462v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:36:33,074] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:36:33,078] [INFO] DFAST_QC result json was written to GCA_022744625.1_ASM2274462v1_genomic.fna/dqc_result.json
[2023-06-13 10:36:33,078] [INFO] DFAST_QC completed!
[2023-06-13 10:36:33,078] [INFO] Total running time: 0h0m52s