[2024-01-25 20:23:50,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:50,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:50,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference
[2024-01-25 20:23:51,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:51,762] [INFO] Task started: Prodigal
[2024-01-25 20:23:51,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f7ef678-5041-456e-848e-97246159fd9f/GCF_009299505.1_ASM929950v1_genomic.fna.gz | prodigal -d GCF_009299505.1_ASM929950v1_genomic.fna/cds.fna -a GCF_009299505.1_ASM929950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:00,472] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:00,472] [INFO] Task started: HMMsearch
[2024-01-25 20:24:00,472] [INFO] Running command: hmmsearch --tblout GCF_009299505.1_ASM929950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference/reference_markers.hmm GCF_009299505.1_ASM929950v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:00,695] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:00,696] [INFO] Found 6/6 markers.
[2024-01-25 20:24:00,721] [INFO] Query marker FASTA was written to GCF_009299505.1_ASM929950v1_genomic.fna/markers.fasta
[2024-01-25 20:24:00,722] [INFO] Task started: Blastn
[2024-01-25 20:24:00,722] [INFO] Running command: blastn -query GCF_009299505.1_ASM929950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference/reference_markers.fasta -out GCF_009299505.1_ASM929950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:01,664] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:01,670] [INFO] Selected 13 target genomes.
[2024-01-25 20:24:01,670] [INFO] Target genome list was writen to GCF_009299505.1_ASM929950v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:01,680] [INFO] Task started: fastANI
[2024-01-25 20:24:01,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7ef678-5041-456e-848e-97246159fd9f/GCF_009299505.1_ASM929950v1_genomic.fna.gz --refList GCF_009299505.1_ASM929950v1_genomic.fna/target_genomes.txt --output GCF_009299505.1_ASM929950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:10,432] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:10,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:10,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:10,441] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:24:10,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:10,442] [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 ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	100.0	995	996	95	conclusive
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	99.984	984	996	95	conclusive
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	88.4752	710	996	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	88.0091	684	996	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	87.3996	676	996	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	87.118	657	996	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	86.9502	637	996	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	84.1686	557	996	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	83.9461	581	996	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.48	543	996	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.2728	312	996	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.082	141	996	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	76.2489	107	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:10,443] [INFO] DFAST Taxonomy check result was written to GCF_009299505.1_ASM929950v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:10,444] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:10,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:10,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference/checkm_data
[2024-01-25 20:24:10,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:10,477] [INFO] Task started: CheckM
[2024-01-25 20:24:10,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009299505.1_ASM929950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009299505.1_ASM929950v1_genomic.fna/checkm_input GCF_009299505.1_ASM929950v1_genomic.fna/checkm_result
[2024-01-25 20:24:41,635] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:41,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:41,653] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:41,653] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:41,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009299505.1_ASM929950v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:41,654] [INFO] Task started: Blastn
[2024-01-25 20:24:41,654] [INFO] Running command: blastn -query GCF_009299505.1_ASM929950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ce2f34d-e343-4c64-ac79-84b2e6dcadfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_009299505.1_ASM929950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:43,096] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:43,099] [INFO] Selected 8 target genomes.
[2024-01-25 20:24:43,099] [INFO] Target genome list was writen to GCF_009299505.1_ASM929950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:43,113] [INFO] Task started: fastANI
[2024-01-25 20:24:43,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7ef678-5041-456e-848e-97246159fd9f/GCF_009299505.1_ASM929950v1_genomic.fna.gz --refList GCF_009299505.1_ASM929950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009299505.1_ASM929950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:49,322] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:49,328] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:49,328] [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_009299505.1	s__Bifidobacterium ramosum	100.0	995	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_018555335.1	s__Bifidobacterium sp018555335	88.5847	698	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667685.1	s__Bifidobacterium aerophilum	87.9894	685	996	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	87.1234	657	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	84.1726	569	996	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	84.0397	588	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_003952945.1	s__Bifidobacterium samirii	83.805	525	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009078285.1	s__Bifidobacterium jacchi	82.5217	469	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:49,329] [INFO] GTDB search result was written to GCF_009299505.1_ASM929950v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:49,330] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:49,332] [INFO] DFAST_QC result json was written to GCF_009299505.1_ASM929950v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:49,332] [INFO] DFAST_QC completed!
[2024-01-25 20:24:49,332] [INFO] Total running time: 0h0m59s