[2024-01-25 20:02:05,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference
[2024-01-25 20:02:06,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:06,632] [INFO] Task started: Prodigal
[2024-01-25 20:02:06,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a1ffd49-b51a-433a-ba50-c88cc2d29e85/GCF_002802875.1_Spades_TRE1_genomic.fna.gz | prodigal -d GCF_002802875.1_Spades_TRE1_genomic.fna/cds.fna -a GCF_002802875.1_Spades_TRE1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:14,362] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:14,362] [INFO] Task started: HMMsearch
[2024-01-25 20:02:14,362] [INFO] Running command: hmmsearch --tblout GCF_002802875.1_Spades_TRE1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference/reference_markers.hmm GCF_002802875.1_Spades_TRE1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:14,557] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:14,558] [INFO] Found 6/6 markers.
[2024-01-25 20:02:14,582] [INFO] Query marker FASTA was written to GCF_002802875.1_Spades_TRE1_genomic.fna/markers.fasta
[2024-01-25 20:02:14,583] [INFO] Task started: Blastn
[2024-01-25 20:02:14,583] [INFO] Running command: blastn -query GCF_002802875.1_Spades_TRE1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference/reference_markers.fasta -out GCF_002802875.1_Spades_TRE1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:15,513] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:15,516] [INFO] Selected 14 target genomes.
[2024-01-25 20:02:15,516] [INFO] Target genome list was writen to GCF_002802875.1_Spades_TRE1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:15,524] [INFO] Task started: fastANI
[2024-01-25 20:02:15,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a1ffd49-b51a-433a-ba50-c88cc2d29e85/GCF_002802875.1_Spades_TRE1_genomic.fna.gz --refList GCF_002802875.1_Spades_TRE1_genomic.fna/target_genomes.txt --output GCF_002802875.1_Spades_TRE1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:24,669] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:24,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:24,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:24,679] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:24,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:24,680] [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 primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	100.0	894	894	95	conclusive
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	94.8098	785	894	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	88.5333	719	894	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	86.3634	626	894	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	85.0688	559	894	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	84.4066	596	894	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	82.423	425	894	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	82.1398	412	894	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.482	427	894	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.4718	409	894	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	81.2815	355	894	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	77.5585	83	894	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	75.9633	98	894	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.794	130	894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:24,681] [INFO] DFAST Taxonomy check result was written to GCF_002802875.1_Spades_TRE1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:24,682] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:24,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:24,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference/checkm_data
[2024-01-25 20:02:24,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:24,712] [INFO] Task started: CheckM
[2024-01-25 20:02:24,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002802875.1_Spades_TRE1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002802875.1_Spades_TRE1_genomic.fna/checkm_input GCF_002802875.1_Spades_TRE1_genomic.fna/checkm_result
[2024-01-25 20:02:52,991] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:52,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:53,021] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:53,022] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:53,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002802875.1_Spades_TRE1_genomic.fna/markers.fasta)
[2024-01-25 20:02:53,022] [INFO] Task started: Blastn
[2024-01-25 20:02:53,022] [INFO] Running command: blastn -query GCF_002802875.1_Spades_TRE1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06580ec9-1dfa-406b-9338-1e086de26a6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002802875.1_Spades_TRE1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:54,439] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:54,454] [INFO] Selected 13 target genomes.
[2024-01-25 20:02:54,454] [INFO] Target genome list was writen to GCF_002802875.1_Spades_TRE1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:54,465] [INFO] Task started: fastANI
[2024-01-25 20:02:54,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a1ffd49-b51a-433a-ba50-c88cc2d29e85/GCF_002802875.1_Spades_TRE1_genomic.fna.gz --refList GCF_002802875.1_Spades_TRE1_genomic.fna/target_genomes_gtdb.txt --output GCF_002802875.1_Spades_TRE1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:02,587] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:02,596] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:02,596] [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_002802875.1	s__Galliscardovia primatium	100.0	894	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010667655.1	s__Galliscardovia saimiriisciurei	94.8202	784	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003129925.1	s__Galliscardovia catulorum	86.37	626	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	85.0467	561	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_003952005.1	s__Galliscardovia callimiconis	84.3802	597	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_002234915.1	s__Galliscardovia vansinderenii	84.3684	599	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860355.1	s__Galliscardovia margollesii	82.9568	486	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	82.4379	424	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	82.2859	429	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	82.0746	442	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932365.1	s__Bifidobacterium sp012932365	82.0223	421	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	82.0001	420	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	81.9086	408	894	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 20:03:02,597] [INFO] GTDB search result was written to GCF_002802875.1_Spades_TRE1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:02,598] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:02,601] [INFO] DFAST_QC result json was written to GCF_002802875.1_Spades_TRE1_genomic.fna/dqc_result.json
[2024-01-25 20:03:02,601] [INFO] DFAST_QC completed!
[2024-01-25 20:03:02,601] [INFO] Total running time: 0h0m57s