[2023-06-13 23:47:16,624] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:47:16,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:47:16,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference
[2023-06-13 23:47:17,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:47:17,723] [INFO] Task started: Prodigal
[2023-06-13 23:47:17,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbe3a3d9-c4b8-472a-9472-06553b1315c3/GCA_022727215.1_ASM2272721v1_genomic.fna.gz | prodigal -d GCA_022727215.1_ASM2272721v1_genomic.fna/cds.fna -a GCA_022727215.1_ASM2272721v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:47:22,045] [INFO] Task succeeded: Prodigal
[2023-06-13 23:47:22,045] [INFO] Task started: HMMsearch
[2023-06-13 23:47:22,045] [INFO] Running command: hmmsearch --tblout GCA_022727215.1_ASM2272721v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference/reference_markers.hmm GCA_022727215.1_ASM2272721v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:47:22,216] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:47:22,217] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdbe3a3d9-c4b8-472a-9472-06553b1315c3/GCA_022727215.1_ASM2272721v1_genomic.fna.gz]
[2023-06-13 23:47:22,234] [INFO] Query marker FASTA was written to GCA_022727215.1_ASM2272721v1_genomic.fna/markers.fasta
[2023-06-13 23:47:22,235] [INFO] Task started: Blastn
[2023-06-13 23:47:22,235] [INFO] Running command: blastn -query GCA_022727215.1_ASM2272721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference/reference_markers.fasta -out GCA_022727215.1_ASM2272721v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:47:22,895] [INFO] Task succeeded: Blastn
[2023-06-13 23:47:22,899] [INFO] Selected 13 target genomes.
[2023-06-13 23:47:22,899] [INFO] Target genome list was writen to GCA_022727215.1_ASM2272721v1_genomic.fna/target_genomes.txt
[2023-06-13 23:47:22,900] [INFO] Task started: fastANI
[2023-06-13 23:47:22,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe3a3d9-c4b8-472a-9472-06553b1315c3/GCA_022727215.1_ASM2272721v1_genomic.fna.gz --refList GCA_022727215.1_ASM2272721v1_genomic.fna/target_genomes.txt --output GCA_022727215.1_ASM2272721v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:47:28,142] [INFO] Task succeeded: fastANI
[2023-06-13 23:47:28,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:47:28,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:47:28,150] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 23:47:28,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 23:47:28,150] [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_000158015.1	1685	1685	type	True	98.1018	354	398	95	conclusive
Bifidobacterium breve	strain=JCM 1192	GCA_001025175.1	1685	1685	type	True	98.0687	357	398	95	conclusive
Bifidobacterium breve	strain=DSM 20213	GCA_000771305.1	1685	1685	type	True	98.0286	356	398	95	conclusive
Bifidobacterium breve	strain=NCTC11815	GCA_900637145.1	1685	1685	type	True	98.0032	358	398	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	83.5655	275	398	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	83.4991	270	398	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	82.7879	276	398	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.0739	258	398	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	80.7054	245	398	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.3176	159	398	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.0359	90	398	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 23:47:28,152] [INFO] DFAST Taxonomy check result was written to GCA_022727215.1_ASM2272721v1_genomic.fna/tc_result.tsv
[2023-06-13 23:47:28,152] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:47:28,152] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:47:28,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference/checkm_data
[2023-06-13 23:47:28,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:47:28,173] [INFO] Task started: CheckM
[2023-06-13 23:47:28,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022727215.1_ASM2272721v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022727215.1_ASM2272721v1_genomic.fna/checkm_input GCA_022727215.1_ASM2272721v1_genomic.fna/checkm_result
[2023-06-13 23:47:45,847] [INFO] Task succeeded: CheckM
[2023-06-13 23:47:45,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:47:45,862] [INFO] ===== Completeness check finished =====
[2023-06-13 23:47:45,862] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:47:45,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022727215.1_ASM2272721v1_genomic.fna/markers.fasta)
[2023-06-13 23:47:45,863] [INFO] Task started: Blastn
[2023-06-13 23:47:45,863] [INFO] Running command: blastn -query GCA_022727215.1_ASM2272721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03ffabae-a362-429c-a15c-6c03a085ddec/dqc_reference/reference_markers_gtdb.fasta -out GCA_022727215.1_ASM2272721v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:47:46,890] [INFO] Task succeeded: Blastn
[2023-06-13 23:47:46,894] [INFO] Selected 11 target genomes.
[2023-06-13 23:47:46,894] [INFO] Target genome list was writen to GCA_022727215.1_ASM2272721v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:47:46,894] [INFO] Task started: fastANI
[2023-06-13 23:47:46,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe3a3d9-c4b8-472a-9472-06553b1315c3/GCA_022727215.1_ASM2272721v1_genomic.fna.gz --refList GCA_022727215.1_ASM2272721v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022727215.1_ASM2272721v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:47:51,721] [INFO] Task succeeded: fastANI
[2023-06-13 23:47:51,728] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 23:47:51,728] [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	98.0687	357	398	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_000196555.1	s__Bifidobacterium longum	83.5467	276	398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_000269965.1	s__Bifidobacterium infantis	82.8269	269	398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.0445	251	398	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	81.0159	260	398	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	80.7054	245	398	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	80.53	241	398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_009193305.1	s__Bifidobacterium cebidarum	80.4121	217	398	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	80.1911	218	398	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	79.8568	209	398	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	79.0777	183	398	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 23:47:51,730] [INFO] GTDB search result was written to GCA_022727215.1_ASM2272721v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:47:51,731] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:47:51,734] [INFO] DFAST_QC result json was written to GCA_022727215.1_ASM2272721v1_genomic.fna/dqc_result.json
[2023-06-13 23:47:51,734] [INFO] DFAST_QC completed!
[2023-06-13 23:47:51,734] [INFO] Total running time: 0h0m35s