[2023-06-14 00:12:47,653] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:12:47,660] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:12:47,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference
[2023-06-14 00:12:49,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:12:49,412] [INFO] Task started: Prodigal
[2023-06-14 00:12:49,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg967878cb-345a-4e66-b0cc-4d72954a6120/GCA_022744965.1_ASM2274496v1_genomic.fna.gz | prodigal -d GCA_022744965.1_ASM2274496v1_genomic.fna/cds.fna -a GCA_022744965.1_ASM2274496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:12:53,790] [INFO] Task succeeded: Prodigal
[2023-06-14 00:12:53,790] [INFO] Task started: HMMsearch
[2023-06-14 00:12:53,791] [INFO] Running command: hmmsearch --tblout GCA_022744965.1_ASM2274496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference/reference_markers.hmm GCA_022744965.1_ASM2274496v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:12:54,034] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:12:54,035] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg967878cb-345a-4e66-b0cc-4d72954a6120/GCA_022744965.1_ASM2274496v1_genomic.fna.gz]
[2023-06-14 00:12:54,055] [INFO] Query marker FASTA was written to GCA_022744965.1_ASM2274496v1_genomic.fna/markers.fasta
[2023-06-14 00:12:54,055] [INFO] Task started: Blastn
[2023-06-14 00:12:54,056] [INFO] Running command: blastn -query GCA_022744965.1_ASM2274496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference/reference_markers.fasta -out GCA_022744965.1_ASM2274496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:12:54,725] [INFO] Task succeeded: Blastn
[2023-06-14 00:12:54,728] [INFO] Selected 13 target genomes.
[2023-06-14 00:12:54,728] [INFO] Target genome list was writen to GCA_022744965.1_ASM2274496v1_genomic.fna/target_genomes.txt
[2023-06-14 00:12:54,729] [INFO] Task started: fastANI
[2023-06-14 00:12:54,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg967878cb-345a-4e66-b0cc-4d72954a6120/GCA_022744965.1_ASM2274496v1_genomic.fna.gz --refList GCA_022744965.1_ASM2274496v1_genomic.fna/target_genomes.txt --output GCA_022744965.1_ASM2274496v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:13:01,132] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:01,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:13:01,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:13:01,142] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2023-06-14 00:13:01,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-14 00:13:01,142] [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=JCM 1192	GCA_001025175.1	1685	1685	type	True	98.466	383	420	95	conclusive
Bifidobacterium breve	strain=NCTC11815	GCA_900637145.1	1685	1685	type	True	98.4656	383	420	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000158015.1	1685	1685	type	True	98.4324	383	420	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000771305.1	1685	1685	type	True	98.4088	385	420	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	85.3337	299	420	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	85.1371	304	420	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	85.1054	293	420	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.9993	285	420	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	81.7296	272	420	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.9718	207	420	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.8904	102	420	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.0464	55	420	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:13:01,144] [INFO] DFAST Taxonomy check result was written to GCA_022744965.1_ASM2274496v1_genomic.fna/tc_result.tsv
[2023-06-14 00:13:01,144] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:13:01,145] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:13:01,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference/checkm_data
[2023-06-14 00:13:01,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:13:01,167] [INFO] Task started: CheckM
[2023-06-14 00:13:01,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744965.1_ASM2274496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744965.1_ASM2274496v1_genomic.fna/checkm_input GCA_022744965.1_ASM2274496v1_genomic.fna/checkm_result
[2023-06-14 00:13:18,905] [INFO] Task succeeded: CheckM
[2023-06-14 00:13:18,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.96%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:13:18,922] [INFO] ===== Completeness check finished =====
[2023-06-14 00:13:18,922] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:13:18,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744965.1_ASM2274496v1_genomic.fna/markers.fasta)
[2023-06-14 00:13:18,922] [INFO] Task started: Blastn
[2023-06-14 00:13:18,922] [INFO] Running command: blastn -query GCA_022744965.1_ASM2274496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54c4cfd9-5bd4-489f-af43-3c7b9426350a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744965.1_ASM2274496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:13:19,890] [INFO] Task succeeded: Blastn
[2023-06-14 00:13:19,893] [INFO] Selected 10 target genomes.
[2023-06-14 00:13:19,893] [INFO] Target genome list was writen to GCA_022744965.1_ASM2274496v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:13:19,894] [INFO] Task started: fastANI
[2023-06-14 00:13:19,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg967878cb-345a-4e66-b0cc-4d72954a6120/GCA_022744965.1_ASM2274496v1_genomic.fna.gz --refList GCA_022744965.1_ASM2274496v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744965.1_ASM2274496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:13:24,532] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:24,539] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:13:24,539] [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	98.466	383	420	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	85.2477	301	420	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	85.1054	293	420	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	82.0504	275	420	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	81.8145	283	420	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	81.7296	272	420	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_009193305.1	s__Bifidobacterium cebidarum	81.4533	250	420	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802865.1	s__Bifidobacterium scaligerum	81.0863	234	420	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	80.9536	247	420	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	80.2141	217	420	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:13:24,541] [INFO] GTDB search result was written to GCA_022744965.1_ASM2274496v1_genomic.fna/result_gtdb.tsv
[2023-06-14 00:13:24,542] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:13:24,544] [INFO] DFAST_QC result json was written to GCA_022744965.1_ASM2274496v1_genomic.fna/dqc_result.json
[2023-06-14 00:13:24,545] [INFO] DFAST_QC completed!
[2023-06-14 00:13:24,545] [INFO] Total running time: 0h0m37s