[2024-01-24 13:49:19,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,179] [INFO] DQC Reference Directory: /var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference
[2024-01-24 13:49:20,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,622] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,623] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd0e8a23-f79e-469f-b454-0adadf218e3e/GCF_030811505.1_ASM3081150v1_genomic.fna.gz | prodigal -d GCF_030811505.1_ASM3081150v1_genomic.fna/cds.fna -a GCF_030811505.1_ASM3081150v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:27,332] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:27,333] [INFO] Task started: HMMsearch
[2024-01-24 13:49:27,333] [INFO] Running command: hmmsearch --tblout GCF_030811505.1_ASM3081150v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference/reference_markers.hmm GCF_030811505.1_ASM3081150v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:27,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:27,582] [INFO] Found 6/6 markers.
[2024-01-24 13:49:27,604] [INFO] Query marker FASTA was written to GCF_030811505.1_ASM3081150v1_genomic.fna/markers.fasta
[2024-01-24 13:49:27,604] [INFO] Task started: Blastn
[2024-01-24 13:49:27,604] [INFO] Running command: blastn -query GCF_030811505.1_ASM3081150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference/reference_markers.fasta -out GCF_030811505.1_ASM3081150v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:28,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:28,454] [INFO] Selected 30 target genomes.
[2024-01-24 13:49:28,454] [INFO] Target genome list was writen to GCF_030811505.1_ASM3081150v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:28,464] [INFO] Task started: fastANI
[2024-01-24 13:49:28,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0e8a23-f79e-469f-b454-0adadf218e3e/GCF_030811505.1_ASM3081150v1_genomic.fna.gz --refList GCF_030811505.1_ASM3081150v1_genomic.fna/target_genomes.txt --output GCF_030811505.1_ASM3081150v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:46,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:46,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:46,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:46,554] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:46,554] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:46,554] [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
Trueperella pecoris	strain=19M2397	GCA_014926385.1	2733571	2733571	type	True	79.2948	105	695	95	below_threshold
Arcanobacterium haemolyticum	strain=NCTC8452	GCA_900475915.1	28264	28264	type	True	79.0921	67	695	95	below_threshold
Trueperella pyogenes	strain=NCTC5224	GCA_900460345.1	1661	1661	type	True	77.9543	92	695	95	below_threshold
Trueperella pyogenes	strain=DSM 20630	GCA_014191445.1	1661	1661	type	True	77.8964	83	695	95	below_threshold
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	77.8918	50	695	95	below_threshold
Trueperella bernardiae	strain=LCDC 89-0504	GCA_001469025.1	59561	59561	type	True	77.6694	137	695	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	77.4913	54	695	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	76.7732	58	695	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	76.1241	69	695	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	75.9651	61	695	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	75.8991	75	695	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	75.8864	61	695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,556] [INFO] DFAST Taxonomy check result was written to GCF_030811505.1_ASM3081150v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:46,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:46,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:46,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference/checkm_data
[2024-01-24 13:49:46,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:46,583] [INFO] Task started: CheckM
[2024-01-24 13:49:46,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811505.1_ASM3081150v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811505.1_ASM3081150v1_genomic.fna/checkm_input GCF_030811505.1_ASM3081150v1_genomic.fna/checkm_result
[2024-01-24 13:50:13,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:13,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,289] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:13,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:13,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811505.1_ASM3081150v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:13,291] [INFO] Task started: Blastn
[2024-01-24 13:50:13,291] [INFO] Running command: blastn -query GCF_030811505.1_ASM3081150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda0629c0-6080-48d0-9577-1a063b145745/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811505.1_ASM3081150v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:14,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:14,388] [INFO] Selected 32 target genomes.
[2024-01-24 13:50:14,388] [INFO] Target genome list was writen to GCF_030811505.1_ASM3081150v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:14,408] [INFO] Task started: fastANI
[2024-01-24 13:50:14,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0e8a23-f79e-469f-b454-0adadf218e3e/GCF_030811505.1_ASM3081150v1_genomic.fna.gz --refList GCF_030811505.1_ASM3081150v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811505.1_ASM3081150v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:32,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:32,014] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:32,014] [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_014926385.1	s__Trueperella pecoris	79.4282	106	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	97.88	95.38	0.92	0.88	4	-
GCF_003952265.1	s__Flaviflexus salsibiostraticola	77.8967	50	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460345.1	s__Trueperella pyogenes	77.7865	91	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	98.61	97.91	0.94	0.87	20	-
GCF_001469025.1	s__Trueperella bernardiae	77.6694	137	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCF_006352065.1	s__Georgenia sp006352065	77.5167	50	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_004135385.1	s__Xylanimonas sp004135385	76.9348	63	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	76.8345	64	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_000024965.1	s__Xylanimonas cellulosilytica	76.7346	55	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155575.1	s__Actinotignum timonense	76.6726	53	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	99.14	98.55	0.97	0.96	4	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	76.1338	61	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	76.0909	57	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_009846865.1	s__Xylanimonas puerhi	76.0304	66	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193155.1	s__Georgenia subflava	75.8878	74	695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:32,016] [INFO] GTDB search result was written to GCF_030811505.1_ASM3081150v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:32,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:32,020] [INFO] DFAST_QC result json was written to GCF_030811505.1_ASM3081150v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:32,021] [INFO] DFAST_QC completed!
[2024-01-24 13:50:32,021] [INFO] Total running time: 0h1m13s