[2024-01-24 14:15:02,603] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference
[2024-01-24 14:15:03,995] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:03,996] [INFO] Task started: Prodigal
[2024-01-24 14:15:03,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg49d6a3c7-1921-4528-8115-634db6e66e28/GCF_019331715.1_ASM1933171v1_genomic.fna.gz | prodigal -d GCF_019331715.1_ASM1933171v1_genomic.fna/cds.fna -a GCF_019331715.1_ASM1933171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:13,557] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:13,558] [INFO] Task started: HMMsearch
[2024-01-24 14:15:13,558] [INFO] Running command: hmmsearch --tblout GCF_019331715.1_ASM1933171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference/reference_markers.hmm GCF_019331715.1_ASM1933171v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:13,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:13,869] [INFO] Found 6/6 markers.
[2024-01-24 14:15:13,900] [INFO] Query marker FASTA was written to GCF_019331715.1_ASM1933171v1_genomic.fna/markers.fasta
[2024-01-24 14:15:13,900] [INFO] Task started: Blastn
[2024-01-24 14:15:13,900] [INFO] Running command: blastn -query GCF_019331715.1_ASM1933171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference/reference_markers.fasta -out GCF_019331715.1_ASM1933171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:15,059] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:15,062] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:15,063] [INFO] Target genome list was writen to GCF_019331715.1_ASM1933171v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:15,071] [INFO] Task started: fastANI
[2024-01-24 14:15:15,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d6a3c7-1921-4528-8115-634db6e66e28/GCF_019331715.1_ASM1933171v1_genomic.fna.gz --refList GCF_019331715.1_ASM1933171v1_genomic.fna/target_genomes.txt --output GCF_019331715.1_ASM1933171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:25,167] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:25,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:25,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:25,179] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:25,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:25,180] [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 simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	100.0	943	943	95	conclusive
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	89.2013	662	943	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	88.4951	705	943	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	88.4332	711	943	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	87.1966	641	943	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	87.1827	639	943	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	87.0269	652	943	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	83.8176	499	943	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.0633	507	943	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.0917	299	943	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.6028	116	943	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	75.7938	110	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:25,181] [INFO] DFAST Taxonomy check result was written to GCF_019331715.1_ASM1933171v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:25,182] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:25,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:25,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference/checkm_data
[2024-01-24 14:15:25,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:25,218] [INFO] Task started: CheckM
[2024-01-24 14:15:25,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019331715.1_ASM1933171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019331715.1_ASM1933171v1_genomic.fna/checkm_input GCF_019331715.1_ASM1933171v1_genomic.fna/checkm_result
[2024-01-24 14:15:57,848] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:57,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:57,865] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:57,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:57,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019331715.1_ASM1933171v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:57,866] [INFO] Task started: Blastn
[2024-01-24 14:15:57,866] [INFO] Running command: blastn -query GCF_019331715.1_ASM1933171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5d6e49-f1ec-4c18-b68a-4237a0d0000e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019331715.1_ASM1933171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:59,615] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:59,618] [INFO] Selected 7 target genomes.
[2024-01-24 14:15:59,618] [INFO] Target genome list was writen to GCF_019331715.1_ASM1933171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:59,625] [INFO] Task started: fastANI
[2024-01-24 14:15:59,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d6a3c7-1921-4528-8115-634db6e66e28/GCF_019331715.1_ASM1933171v1_genomic.fna.gz --refList GCF_019331715.1_ASM1933171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019331715.1_ASM1933171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:05,132] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:05,140] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:05,140] [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_018555335.1	s__Bifidobacterium sp018555335	98.1236	841	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010667685.1	s__Bifidobacterium aerophilum	89.1977	662	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299505.1	s__Bifidobacterium ramosum	88.5092	704	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000741165.1	s__Bifidobacterium biavatii	87.0209	653	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_003952945.1	s__Bifidobacterium samirii	83.9349	493	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	83.6702	542	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_009078285.1	s__Bifidobacterium jacchi	82.3939	436	943	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 14:16:05,142] [INFO] GTDB search result was written to GCF_019331715.1_ASM1933171v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:05,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:05,145] [INFO] DFAST_QC result json was written to GCF_019331715.1_ASM1933171v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:05,145] [INFO] DFAST_QC completed!
[2024-01-24 14:16:05,146] [INFO] Total running time: 0h1m3s