[2024-01-24 14:22:01,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference
[2024-01-24 14:22:02,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,881] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,882] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f2ef95-8c5c-4a2c-baeb-6d91d652c518/GCF_002443115.1_ASM244311v1_genomic.fna.gz | prodigal -d GCF_002443115.1_ASM244311v1_genomic.fna/cds.fna -a GCF_002443115.1_ASM244311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:10,840] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:10,841] [INFO] Task started: HMMsearch
[2024-01-24 14:22:10,841] [INFO] Running command: hmmsearch --tblout GCF_002443115.1_ASM244311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference/reference_markers.hmm GCF_002443115.1_ASM244311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:11,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:11,027] [INFO] Found 6/6 markers.
[2024-01-24 14:22:11,048] [INFO] Query marker FASTA was written to GCF_002443115.1_ASM244311v1_genomic.fna/markers.fasta
[2024-01-24 14:22:11,048] [INFO] Task started: Blastn
[2024-01-24 14:22:11,049] [INFO] Running command: blastn -query GCF_002443115.1_ASM244311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference/reference_markers.fasta -out GCF_002443115.1_ASM244311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:11,958] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:11,962] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:11,962] [INFO] Target genome list was writen to GCF_002443115.1_ASM244311v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:11,988] [INFO] Task started: fastANI
[2024-01-24 14:22:11,988] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f2ef95-8c5c-4a2c-baeb-6d91d652c518/GCF_002443115.1_ASM244311v1_genomic.fna.gz --refList GCF_002443115.1_ASM244311v1_genomic.fna/target_genomes.txt --output GCF_002443115.1_ASM244311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:22,378] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:22,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:22,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:22,392] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:22:22,392] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:22:22,393] [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
Dermabacter jinjuensis	strain=32T	GCA_002443115.1	1667168	1667168	type	True	100.0	795	799	95	inconclusive
Dermabacter jinjuensis	strain=FDAARGOS_1555	GCA_020736445.1	1667168	1667168	type	True	99.993	790	799	95	inconclusive
Dermabacter hominis	strain=NBRC 106157	GCA_001570785.1	36740	36740	type	True	95.8293	658	799	95	inconclusive
Dermabacter vaginalis	strain=AD1-86	GCA_001678905.1	1630135	1630135	type	True	87.4154	625	799	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	78.0848	166	799	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	77.6634	175	799	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	77.5765	175	799	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	77.552	160	799	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	77.5219	155	799	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	77.3315	167	799	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	77.1854	66	799	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.6228	79	799	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5538	85	799	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	75.7201	62	799	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	75.6653	59	799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:22,394] [INFO] DFAST Taxonomy check result was written to GCF_002443115.1_ASM244311v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:22,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:22,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:22,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference/checkm_data
[2024-01-24 14:22:22,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:22,423] [INFO] Task started: CheckM
[2024-01-24 14:22:22,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002443115.1_ASM244311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002443115.1_ASM244311v1_genomic.fna/checkm_input GCF_002443115.1_ASM244311v1_genomic.fna/checkm_result
[2024-01-24 14:22:51,289] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:51,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,308] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:51,309] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:51,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002443115.1_ASM244311v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:51,309] [INFO] Task started: Blastn
[2024-01-24 14:22:51,309] [INFO] Running command: blastn -query GCF_002443115.1_ASM244311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15ada834-89fc-43a5-acdd-a039d08412fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002443115.1_ASM244311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:52,605] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:52,609] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:52,609] [INFO] Target genome list was writen to GCF_002443115.1_ASM244311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:52,619] [INFO] Task started: fastANI
[2024-01-24 14:22:52,620] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f2ef95-8c5c-4a2c-baeb-6d91d652c518/GCF_002443115.1_ASM244311v1_genomic.fna.gz --refList GCF_002443115.1_ASM244311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002443115.1_ASM244311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:03,910] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:03,923] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:03,923] [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_001570785.1	s__Dermabacter hominis	95.8293	658	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	96.01	95.75	0.93	0.91	8	conclusive
GCF_001678905.1	s__Dermabacter vaginalis	87.4122	625	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	96.46	96.40	0.93	0.93	3	-
GCF_001403775.1	s__Dermabacter massiliensis_A	84.9234	577	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191425.1	s__Helcobacillus massiliensis	79.5525	182	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Helcobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871795.1	s__Brachybacterium sp002871795	78.2104	156	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163655.1	s__Brachybacterium nesterenkovii	78.0848	166	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005490785.1	s__Brachybacterium sp005490785	77.8037	177	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623465.1	s__Brachybacterium halotolerans	77.552	160	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023405.1	s__Brachybacterium faecium	77.525	155	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130585.1	s__Brachybacterium endophyticum	77.4708	145	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299795.1	s__Brachybacterium subflavum	77.3152	168	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220945.1	s__Amycolatopsis mediterranei	76.8521	68	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCA_019118275.1	s__Brachybacterium merdavium	76.7332	99	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	76.5401	68	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001420995.1	s__Pseudonocardia sp001420995	76.2116	57	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_003937945.1	s__Amycolatopsis eburnea	75.7201	62	799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:03,925] [INFO] GTDB search result was written to GCF_002443115.1_ASM244311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:03,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:03,929] [INFO] DFAST_QC result json was written to GCF_002443115.1_ASM244311v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:03,929] [INFO] DFAST_QC completed!
[2024-01-24 14:23:03,929] [INFO] Total running time: 0h1m2s