[2024-01-24 12:44:33,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:33,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:33,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference
[2024-01-24 12:44:34,313] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:34,314] [INFO] Task started: Prodigal
[2024-01-24 12:44:34,314] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb7b84ad-4fac-4f56-8834-91b4d1a80568/GCF_005405645.1_ASM540564v1_genomic.fna.gz | prodigal -d GCF_005405645.1_ASM540564v1_genomic.fna/cds.fna -a GCF_005405645.1_ASM540564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:42,971] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:42,972] [INFO] Task started: HMMsearch
[2024-01-24 12:44:42,972] [INFO] Running command: hmmsearch --tblout GCF_005405645.1_ASM540564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference/reference_markers.hmm GCF_005405645.1_ASM540564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:43,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:43,237] [INFO] Found 6/6 markers.
[2024-01-24 12:44:43,278] [INFO] Query marker FASTA was written to GCF_005405645.1_ASM540564v1_genomic.fna/markers.fasta
[2024-01-24 12:44:43,279] [INFO] Task started: Blastn
[2024-01-24 12:44:43,279] [INFO] Running command: blastn -query GCF_005405645.1_ASM540564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference/reference_markers.fasta -out GCF_005405645.1_ASM540564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:44,348] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:44,353] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:44,353] [INFO] Target genome list was writen to GCF_005405645.1_ASM540564v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:44,388] [INFO] Task started: fastANI
[2024-01-24 12:44:44,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb7b84ad-4fac-4f56-8834-91b4d1a80568/GCF_005405645.1_ASM540564v1_genomic.fna.gz --refList GCF_005405645.1_ASM540564v1_genomic.fna/target_genomes.txt --output GCF_005405645.1_ASM540564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:51,109] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:51,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:51,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:51,120] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:51,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:51,120] [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 moukalabense	strain=GG01	GCA_005405645.1	1333651	1333651	type	True	100.0	829	830	95	conclusive
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	99.9855	813	830	95	conclusive
Bifidobacterium dentium	strain=DSM 20436	GCA_000771725.1	1689	1689	type	True	89.3853	675	830	95	below_threshold
Bifidobacterium dentium	strain=DSM 20436	GCA_900105745.1	1689	1689	type	True	89.3758	685	830	95	below_threshold
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	89.3421	692	830	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000771545.1	630129	1686	type	True	82.1041	432	830	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	82.0811	442	830	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	82.07	448	830	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.8382	381	830	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.396	384	830	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.8907	265	830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:51,121] [INFO] DFAST Taxonomy check result was written to GCF_005405645.1_ASM540564v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:51,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:51,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:51,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference/checkm_data
[2024-01-24 12:44:51,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:51,150] [INFO] Task started: CheckM
[2024-01-24 12:44:51,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405645.1_ASM540564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405645.1_ASM540564v1_genomic.fna/checkm_input GCF_005405645.1_ASM540564v1_genomic.fna/checkm_result
[2024-01-24 12:45:21,766] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:21,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:21,787] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:21,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:21,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405645.1_ASM540564v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:21,789] [INFO] Task started: Blastn
[2024-01-24 12:45:21,789] [INFO] Running command: blastn -query GCF_005405645.1_ASM540564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg130d7f20-c70a-4248-a4f3-917c8dfead4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405645.1_ASM540564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:23,123] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:23,126] [INFO] Selected 10 target genomes.
[2024-01-24 12:45:23,126] [INFO] Target genome list was writen to GCF_005405645.1_ASM540564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:23,139] [INFO] Task started: fastANI
[2024-01-24 12:45:23,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb7b84ad-4fac-4f56-8834-91b4d1a80568/GCF_005405645.1_ASM540564v1_genomic.fna.gz --refList GCF_005405645.1_ASM540564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405645.1_ASM540564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:28,268] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:28,277] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:28,278] [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_000522505.1	s__Bifidobacterium moukalabense	99.9855	813	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	conclusive
GCF_001042595.1	s__Bifidobacterium dentium	89.3421	692	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_000010425.1	s__Bifidobacterium adolescentis	83.5069	478	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCA_002451435.1	s__Bifidobacterium sp002451435	83.1187	393	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000770925.1	s__Bifidobacterium ruminantium	83.0321	457	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	82.4354	453	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_002742445.1	s__Bifidobacterium sp002742445	82.2645	428	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_001025195.1	s__Bifidobacterium catenulatum	82.2472	434	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	82.0579	449	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	82.0098	458	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:28,280] [INFO] GTDB search result was written to GCF_005405645.1_ASM540564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:28,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:28,283] [INFO] DFAST_QC result json was written to GCF_005405645.1_ASM540564v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:28,283] [INFO] DFAST_QC completed!
[2024-01-24 12:45:28,284] [INFO] Total running time: 0h0m55s