[2023-06-19 00:26:14,485] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:26:14,535] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:26:14,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference
[2023-06-19 00:26:15,802] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:26:15,803] [INFO] Task started: Prodigal
[2023-06-19 00:26:15,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f69064e-b3c8-45eb-8c6b-fd8c013681df/GCA_018381665.1_ASM1838166v1_genomic.fna.gz | prodigal -d GCA_018381665.1_ASM1838166v1_genomic.fna/cds.fna -a GCA_018381665.1_ASM1838166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:26:22,607] [INFO] Task succeeded: Prodigal
[2023-06-19 00:26:22,608] [INFO] Task started: HMMsearch
[2023-06-19 00:26:22,608] [INFO] Running command: hmmsearch --tblout GCA_018381665.1_ASM1838166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference/reference_markers.hmm GCA_018381665.1_ASM1838166v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:26:22,793] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:26:22,796] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8f69064e-b3c8-45eb-8c6b-fd8c013681df/GCA_018381665.1_ASM1838166v1_genomic.fna.gz]
[2023-06-19 00:26:22,816] [INFO] Query marker FASTA was written to GCA_018381665.1_ASM1838166v1_genomic.fna/markers.fasta
[2023-06-19 00:26:22,817] [INFO] Task started: Blastn
[2023-06-19 00:26:22,817] [INFO] Running command: blastn -query GCA_018381665.1_ASM1838166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference/reference_markers.fasta -out GCA_018381665.1_ASM1838166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:26:23,519] [INFO] Task succeeded: Blastn
[2023-06-19 00:26:23,525] [INFO] Selected 16 target genomes.
[2023-06-19 00:26:23,526] [INFO] Target genome list was writen to GCA_018381665.1_ASM1838166v1_genomic.fna/target_genomes.txt
[2023-06-19 00:26:23,528] [INFO] Task started: fastANI
[2023-06-19 00:26:23,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f69064e-b3c8-45eb-8c6b-fd8c013681df/GCA_018381665.1_ASM1838166v1_genomic.fna.gz --refList GCA_018381665.1_ASM1838166v1_genomic.fna/target_genomes.txt --output GCA_018381665.1_ASM1838166v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:26:30,999] [INFO] Task succeeded: fastANI
[2023-06-19 00:26:30,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:26:30,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:26:31,010] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:26:31,011] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:26:31,011] [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 catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	94.0469	544	642	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	94.0403	549	642	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000771545.1	630129	1686	type	True	94.0254	541	642	95	below_threshold
Bifidobacterium catenulatum	strain=JCM 1194	GCA_001025195.1	1686	1686	type	True	93.5263	526	642	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000173455.1	1686	1686	type	True	93.4076	523	642	95	below_threshold
Bifidobacterium catenulatum	strain=LMG 11043	GCA_000741565.1	1686	1686	type	True	93.4029	518	642	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	93.3957	499	642	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000173435.1	28026	28026	type	True	92.3435	541	642	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	92.3114	546	642	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.7521	260	642	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.484	264	642	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.3242	179	642	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	76.7913	80	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:26:31,013] [INFO] DFAST Taxonomy check result was written to GCA_018381665.1_ASM1838166v1_genomic.fna/tc_result.tsv
[2023-06-19 00:26:31,013] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:26:31,014] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:26:31,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference/checkm_data
[2023-06-19 00:26:31,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:26:31,038] [INFO] Task started: CheckM
[2023-06-19 00:26:31,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018381665.1_ASM1838166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018381665.1_ASM1838166v1_genomic.fna/checkm_input GCA_018381665.1_ASM1838166v1_genomic.fna/checkm_result
[2023-06-19 00:26:56,139] [INFO] Task succeeded: CheckM
[2023-06-19 00:26:56,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.14%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 00:26:56,164] [INFO] ===== Completeness check finished =====
[2023-06-19 00:26:56,164] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:26:56,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018381665.1_ASM1838166v1_genomic.fna/markers.fasta)
[2023-06-19 00:26:56,165] [INFO] Task started: Blastn
[2023-06-19 00:26:56,165] [INFO] Running command: blastn -query GCA_018381665.1_ASM1838166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a211dbd-3b1e-4142-a2a7-64d85766cbb3/dqc_reference/reference_markers_gtdb.fasta -out GCA_018381665.1_ASM1838166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:26:57,129] [INFO] Task succeeded: Blastn
[2023-06-19 00:26:57,134] [INFO] Selected 9 target genomes.
[2023-06-19 00:26:57,134] [INFO] Target genome list was writen to GCA_018381665.1_ASM1838166v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:26:57,139] [INFO] Task started: fastANI
[2023-06-19 00:26:57,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f69064e-b3c8-45eb-8c6b-fd8c013681df/GCA_018381665.1_ASM1838166v1_genomic.fna.gz --refList GCA_018381665.1_ASM1838166v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018381665.1_ASM1838166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:27:01,443] [INFO] Task succeeded: fastANI
[2023-06-19 00:27:01,451] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:27:01,452] [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_002742445.1	s__Bifidobacterium sp002742445	97.093	558	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	conclusive
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	94.1814	543	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	94.0469	544	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_001025195.1	s__Bifidobacterium catenulatum	93.4983	527	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	92.2509	544	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_000010425.1	s__Bifidobacterium adolescentis	83.6746	434	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_000770925.1	s__Bifidobacterium ruminantium	82.2861	422	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCA_002451435.1	s__Bifidobacterium sp002451435	82.1323	350	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000522505.1	s__Bifidobacterium moukalabense	81.8834	411	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
--------------------------------------------------------------------------------
[2023-06-19 00:27:01,459] [INFO] GTDB search result was written to GCA_018381665.1_ASM1838166v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:27:01,460] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:27:01,464] [INFO] DFAST_QC result json was written to GCA_018381665.1_ASM1838166v1_genomic.fna/dqc_result.json
[2023-06-19 00:27:01,464] [INFO] DFAST_QC completed!
[2023-06-19 00:27:01,464] [INFO] Total running time: 0h0m47s