[2024-01-25 18:47:35,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:35,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:35,637] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference
[2024-01-25 18:47:36,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:36,838] [INFO] Task started: Prodigal
[2024-01-25 18:47:36,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d434817-b2ae-405b-b97e-03220b7bf992/GCF_000706765.1_ASM70676v1_genomic.fna.gz | prodigal -d GCF_000706765.1_ASM70676v1_genomic.fna/cds.fna -a GCF_000706765.1_ASM70676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:41,677] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:41,677] [INFO] Task started: HMMsearch
[2024-01-25 18:47:41,677] [INFO] Running command: hmmsearch --tblout GCF_000706765.1_ASM70676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference/reference_markers.hmm GCF_000706765.1_ASM70676v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:41,872] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:41,873] [INFO] Found 6/6 markers.
[2024-01-25 18:47:41,894] [INFO] Query marker FASTA was written to GCF_000706765.1_ASM70676v1_genomic.fna/markers.fasta
[2024-01-25 18:47:41,895] [INFO] Task started: Blastn
[2024-01-25 18:47:41,895] [INFO] Running command: blastn -query GCF_000706765.1_ASM70676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference/reference_markers.fasta -out GCF_000706765.1_ASM70676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:42,589] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:42,592] [INFO] Selected 11 target genomes.
[2024-01-25 18:47:42,593] [INFO] Target genome list was writen to GCF_000706765.1_ASM70676v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:42,601] [INFO] Task started: fastANI
[2024-01-25 18:47:42,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d434817-b2ae-405b-b97e-03220b7bf992/GCF_000706765.1_ASM70676v1_genomic.fna.gz --refList GCF_000706765.1_ASM70676v1_genomic.fna/target_genomes.txt --output GCF_000706765.1_ASM70676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:49,356] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:49,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:49,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:49,363] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:47:49,363] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:47:49,363] [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 indicum	strain=LMG 11587	GCA_000706765.1	1691	1691	suspected-type	True	100.0	575	578	95	inconclusive
Bifidobacterium indicum	strain=DSM 20214	GCA_000771325.1	1691	1691	suspected-type	True	99.9775	558	578	95	inconclusive
Bifidobacterium coryneforme	strain=LMG18911	GCA_000737865.1	1687	1687	suspected-type	True	98.2608	560	578	95	inconclusive
Bifidobacterium coryneforme	strain=DSM 20216	GCA_000771345.1	1687	1687	suspected-type	True	98.2489	537	578	95	inconclusive
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	81.0072	341	578	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	80.9503	342	578	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	80.8198	354	578	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.8562	140	578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:49,364] [INFO] DFAST Taxonomy check result was written to GCF_000706765.1_ASM70676v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:49,365] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:49,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:49,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference/checkm_data
[2024-01-25 18:47:49,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:49,387] [INFO] Task started: CheckM
[2024-01-25 18:47:49,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000706765.1_ASM70676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000706765.1_ASM70676v1_genomic.fna/checkm_input GCF_000706765.1_ASM70676v1_genomic.fna/checkm_result
[2024-01-25 18:48:08,491] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:08,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:08,513] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:08,514] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:08,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000706765.1_ASM70676v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:08,516] [INFO] Task started: Blastn
[2024-01-25 18:48:08,516] [INFO] Running command: blastn -query GCF_000706765.1_ASM70676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b70ad4-79b7-4407-9821-dbcb82efe9d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000706765.1_ASM70676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:09,518] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:09,521] [INFO] Selected 13 target genomes.
[2024-01-25 18:48:09,521] [INFO] Target genome list was writen to GCF_000706765.1_ASM70676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:09,532] [INFO] Task started: fastANI
[2024-01-25 18:48:09,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d434817-b2ae-405b-b97e-03220b7bf992/GCF_000706765.1_ASM70676v1_genomic.fna.gz --refList GCF_000706765.1_ASM70676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000706765.1_ASM70676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:17,020] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:17,027] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:17,027] [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_000706765.1	s__Bifidobacterium indicum	100.0	576	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.17	97.45	0.96	0.94	8	conclusive
GCF_016100725.1	s__Bifidobacterium sp016100725	81.231	343	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.87	96.39	0.95	0.91	9	-
GCF_000967185.1	s__Bifidobacterium asteroides_B	81.0046	346	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	80.9191	341	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_000499285.1	s__Bifidobacterium sp000499285	80.9171	333	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000499185.1	s__Bifidobacterium sp000499185	80.8287	350	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.45	96.45	0.89	0.89	2	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	80.7934	335	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202755.1	s__Bifidobacterium asteroides_F	80.578	320	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202715.1	s__Bifidobacterium asteroides_E	80.408	331	578	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.91	96.34	0.93	0.92	10	-
GCF_003202695.1	s__Bifidobacterium asteroides_G	80.2577	324	578	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 18:48:17,029] [INFO] GTDB search result was written to GCF_000706765.1_ASM70676v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:17,029] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:17,032] [INFO] DFAST_QC result json was written to GCF_000706765.1_ASM70676v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:17,032] [INFO] DFAST_QC completed!
[2024-01-25 18:48:17,032] [INFO] Total running time: 0h0m41s