[2024-01-24 13:57:42,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference
[2024-01-24 13:57:44,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,062] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg33e95c2b-c0e1-4327-9a50-4ebbee05155e/GCF_016101585.1_ASM1610158v1_genomic.fna.gz | prodigal -d GCF_016101585.1_ASM1610158v1_genomic.fna/cds.fna -a GCF_016101585.1_ASM1610158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:51,249] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:51,250] [INFO] Task started: HMMsearch
[2024-01-24 13:57:51,250] [INFO] Running command: hmmsearch --tblout GCF_016101585.1_ASM1610158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference/reference_markers.hmm GCF_016101585.1_ASM1610158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:51,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:51,492] [INFO] Found 6/6 markers.
[2024-01-24 13:57:51,519] [INFO] Query marker FASTA was written to GCF_016101585.1_ASM1610158v1_genomic.fna/markers.fasta
[2024-01-24 13:57:51,520] [INFO] Task started: Blastn
[2024-01-24 13:57:51,520] [INFO] Running command: blastn -query GCF_016101585.1_ASM1610158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference/reference_markers.fasta -out GCF_016101585.1_ASM1610158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:52,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:52,262] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:52,263] [INFO] Target genome list was writen to GCF_016101585.1_ASM1610158v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:52,283] [INFO] Task started: fastANI
[2024-01-24 13:57:52,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e95c2b-c0e1-4327-9a50-4ebbee05155e/GCF_016101585.1_ASM1610158v1_genomic.fna.gz --refList GCF_016101585.1_ASM1610158v1_genomic.fna/target_genomes.txt --output GCF_016101585.1_ASM1610158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:58,089] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:58,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:58,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:58,099] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:58,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:58,099] [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 polysaccharolyticum	strain=W8117	GCA_016101585.1	2750967	2750967	type	True	100.0	737	738	95	conclusive
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	91.5705	562	738	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	91.5489	590	738	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	91.228	580	738	95	below_threshold
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	90.8478	550	738	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	90.6305	555	738	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	78.2617	170	738	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.3958	91	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:58,101] [INFO] DFAST Taxonomy check result was written to GCF_016101585.1_ASM1610158v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:58,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:58,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:58,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference/checkm_data
[2024-01-24 13:57:58,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:58,133] [INFO] Task started: CheckM
[2024-01-24 13:57:58,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016101585.1_ASM1610158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016101585.1_ASM1610158v1_genomic.fna/checkm_input GCF_016101585.1_ASM1610158v1_genomic.fna/checkm_result
[2024-01-24 13:58:25,396] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:25,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,422] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:25,423] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:25,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016101585.1_ASM1610158v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:25,424] [INFO] Task started: Blastn
[2024-01-24 13:58:25,425] [INFO] Running command: blastn -query GCF_016101585.1_ASM1610158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg128bf3bd-eb0d-4220-a7a7-dd6ba10d2eab/dqc_reference/reference_markers_gtdb.fasta -out GCF_016101585.1_ASM1610158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:26,432] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:26,440] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:26,440] [INFO] Target genome list was writen to GCF_016101585.1_ASM1610158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:26,449] [INFO] Task started: fastANI
[2024-01-24 13:58:26,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e95c2b-c0e1-4327-9a50-4ebbee05155e/GCF_016101585.1_ASM1610158v1_genomic.fna.gz --refList GCF_016101585.1_ASM1610158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016101585.1_ASM1610158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:31,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:31,491] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:31,491] [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_003202715.1	s__Bifidobacterium asteroides_E	97.0411	685	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.91	96.34	0.93	0.92	10	conclusive
GCF_003202755.1	s__Bifidobacterium asteroides_F	93.5034	573	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002715865.1	s__Bifidobacterium asteroides	91.5491	590	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.35	97.73	0.95	0.92	9	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	91.5426	592	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	91.1993	571	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016100725.1	s__Bifidobacterium sp016100725	91.1284	583	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.87	96.39	0.95	0.91	9	-
GCF_000499285.1	s__Bifidobacterium sp000499285	90.8725	588	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967185.1	s__Bifidobacterium asteroides_B	90.8638	564	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_000499185.1	s__Bifidobacterium sp000499185	90.4624	545	738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.45	96.45	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:31,493] [INFO] GTDB search result was written to GCF_016101585.1_ASM1610158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:31,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:31,498] [INFO] DFAST_QC result json was written to GCF_016101585.1_ASM1610158v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:31,498] [INFO] DFAST_QC completed!
[2024-01-24 13:58:31,498] [INFO] Total running time: 0h0m49s