[2023-06-29 04:44:46,980] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:44:46,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:44:46,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference
[2023-06-29 04:44:49,231] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:44:49,232] [INFO] Task started: Prodigal
[2023-06-29 04:44:49,233] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cc5ec5d-2bc3-4cba-9f5d-0b7870ead8c4/GCA_012719795.1_ASM1271979v1_genomic.fna.gz | prodigal -d GCA_012719795.1_ASM1271979v1_genomic.fna/cds.fna -a GCA_012719795.1_ASM1271979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:44:56,842] [INFO] Task succeeded: Prodigal
[2023-06-29 04:44:56,843] [INFO] Task started: HMMsearch
[2023-06-29 04:44:56,843] [INFO] Running command: hmmsearch --tblout GCA_012719795.1_ASM1271979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference/reference_markers.hmm GCA_012719795.1_ASM1271979v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:44:57,075] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:44:57,077] [INFO] Found 6/6 markers.
[2023-06-29 04:44:57,101] [INFO] Query marker FASTA was written to GCA_012719795.1_ASM1271979v1_genomic.fna/markers.fasta
[2023-06-29 04:44:57,101] [INFO] Task started: Blastn
[2023-06-29 04:44:57,101] [INFO] Running command: blastn -query GCA_012719795.1_ASM1271979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference/reference_markers.fasta -out GCA_012719795.1_ASM1271979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:44:57,876] [INFO] Task succeeded: Blastn
[2023-06-29 04:44:57,881] [INFO] Selected 22 target genomes.
[2023-06-29 04:44:57,881] [INFO] Target genome list was writen to GCA_012719795.1_ASM1271979v1_genomic.fna/target_genomes.txt
[2023-06-29 04:44:57,887] [INFO] Task started: fastANI
[2023-06-29 04:44:57,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cc5ec5d-2bc3-4cba-9f5d-0b7870ead8c4/GCA_012719795.1_ASM1271979v1_genomic.fna.gz --refList GCA_012719795.1_ASM1271979v1_genomic.fna/target_genomes.txt --output GCA_012719795.1_ASM1271979v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:45:07,555] [INFO] Task succeeded: fastANI
[2023-06-29 04:45:07,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:45:07,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:45:07,575] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 04:45:07,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 04:45:07,576] [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 crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	97.4715	688	766	95	conclusive
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_000771565.1	218140	218140	type	True	80.5504	387	766	95	below_threshold
Bifidobacterium psychraerophilum	strain=LMG 21775	GCA_000741705.1	218140	218140	type	True	80.521	387	766	95	below_threshold
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_002813205.1	218140	218140	type	True	80.4737	401	766	95	below_threshold
Bifidobacterium aquikefiri	strain=LMG 28769	GCA_002259795.1	1653207	1653207	type	True	77.9841	120	766	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	77.7644	138	766	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_014898155.1	1765219	1765219	type	True	77.5123	145	766	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000771645.1	762212	762212	type	True	77.4733	115	766	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	77.4217	113	766	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.3959	102	766	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_002259685.1	1765219	1765219	type	True	77.394	151	766	95	below_threshold
Bifidobacterium cebidarum	strain=LMG 31469	GCA_009193305.1	2650773	2650773	type	True	77.3783	132	766	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.3692	152	766	95	below_threshold
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	77.3381	145	766	95	below_threshold
Bifidobacterium actinocoloniiforme	strain=DSM 22766	GCA_000771585.1	638619	638619	type	True	77.3301	84	766	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	77.2587	110	766	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	77.2398	106	766	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	77.0908	108	766	95	below_threshold
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	77.0651	108	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:45:07,578] [INFO] DFAST Taxonomy check result was written to GCA_012719795.1_ASM1271979v1_genomic.fna/tc_result.tsv
[2023-06-29 04:45:07,578] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:45:07,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:45:07,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference/checkm_data
[2023-06-29 04:45:07,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:45:07,608] [INFO] Task started: CheckM
[2023-06-29 04:45:07,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012719795.1_ASM1271979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012719795.1_ASM1271979v1_genomic.fna/checkm_input GCA_012719795.1_ASM1271979v1_genomic.fna/checkm_result
[2023-06-29 04:45:35,110] [INFO] Task succeeded: CheckM
[2023-06-29 04:45:35,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:45:35,132] [INFO] ===== Completeness check finished =====
[2023-06-29 04:45:35,132] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:45:35,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012719795.1_ASM1271979v1_genomic.fna/markers.fasta)
[2023-06-29 04:45:35,133] [INFO] Task started: Blastn
[2023-06-29 04:45:35,133] [INFO] Running command: blastn -query GCA_012719795.1_ASM1271979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cb8fb23-cb19-423c-b781-96af37254557/dqc_reference/reference_markers_gtdb.fasta -out GCA_012719795.1_ASM1271979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:45:36,188] [INFO] Task succeeded: Blastn
[2023-06-29 04:45:36,193] [INFO] Selected 25 target genomes.
[2023-06-29 04:45:36,193] [INFO] Target genome list was writen to GCA_012719795.1_ASM1271979v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:45:36,208] [INFO] Task started: fastANI
[2023-06-29 04:45:36,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cc5ec5d-2bc3-4cba-9f5d-0b7870ead8c4/GCA_012719795.1_ASM1271979v1_genomic.fna.gz --refList GCA_012719795.1_ASM1271979v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012719795.1_ASM1271979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:45:47,432] [INFO] Task succeeded: fastANI
[2023-06-29 04:45:47,462] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:45:47,462] [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_000738005.1	s__Bifidobacterium crudilactis	97.4715	688	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	conclusive
GCF_000741705.1	s__Bifidobacterium psychraerophilum	80.5056	388	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_002259795.1	s__Bifidobacterium aquikefiri	77.9841	120	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	77.7644	138	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_000706765.1	s__Bifidobacterium indicum	77.6035	98	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.17	97.45	0.96	0.94	8	-
GCF_000770925.1	s__Bifidobacterium ruminantium	77.5904	130	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_014898155.1	s__Bifidobacterium eulemuris	77.5123	145	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000771405.1	s__Bifidobacterium pullorum	77.4765	153	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCA_000771265.1	s__Bifidobacterium thermophilum	77.4609	119	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_008698235.1	s__Bifidobacterium rousetti	77.4351	130	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_001263395.1	s__Bifidobacterium actinocoloniiforme	77.4222	85	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000741165.1	s__Bifidobacterium biavatii	77.4217	113	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_003202755.1	s__Bifidobacterium asteroides_F	77.4029	98	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193305.1	s__Bifidobacterium cebidarum	77.3783	132	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042595.1	s__Bifidobacterium dentium	77.3622	127	766	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	77.3413	132	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	77.3381	145	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000522505.1	s__Bifidobacterium moukalabense	77.3216	136	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_002715865.1	s__Bifidobacterium asteroides	77.2587	110	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.35	97.73	0.95	0.92	9	-
GCF_000499285.1	s__Bifidobacterium sp000499285	77.2409	105	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	77.2079	105	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_002802915.1	s__Bifidobacterium felsineum	77.1367	132	766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-29 04:45:47,464] [INFO] GTDB search result was written to GCA_012719795.1_ASM1271979v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:45:47,465] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:45:47,470] [INFO] DFAST_QC result json was written to GCA_012719795.1_ASM1271979v1_genomic.fna/dqc_result.json
[2023-06-29 04:45:47,470] [INFO] DFAST_QC completed!
[2023-06-29 04:45:47,470] [INFO] Total running time: 0h1m0s