[2024-01-25 18:08:35,669] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference
[2024-01-25 18:08:36,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,797] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg64254382-12b5-4b5e-90e0-3cdd661c9462/GCF_013280495.1_ASM1328049v1_genomic.fna.gz | prodigal -d GCF_013280495.1_ASM1328049v1_genomic.fna/cds.fna -a GCF_013280495.1_ASM1328049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:46,390] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:46,391] [INFO] Task started: HMMsearch
[2024-01-25 18:08:46,391] [INFO] Running command: hmmsearch --tblout GCF_013280495.1_ASM1328049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference/reference_markers.hmm GCF_013280495.1_ASM1328049v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:46,582] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:46,583] [INFO] Found 6/6 markers.
[2024-01-25 18:08:46,612] [INFO] Query marker FASTA was written to GCF_013280495.1_ASM1328049v1_genomic.fna/markers.fasta
[2024-01-25 18:08:46,613] [INFO] Task started: Blastn
[2024-01-25 18:08:46,613] [INFO] Running command: blastn -query GCF_013280495.1_ASM1328049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference/reference_markers.fasta -out GCF_013280495.1_ASM1328049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:47,630] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:47,632] [INFO] Selected 12 target genomes.
[2024-01-25 18:08:47,633] [INFO] Target genome list was writen to GCF_013280495.1_ASM1328049v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:47,647] [INFO] Task started: fastANI
[2024-01-25 18:08:47,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg64254382-12b5-4b5e-90e0-3cdd661c9462/GCF_013280495.1_ASM1328049v1_genomic.fna.gz --refList GCF_013280495.1_ASM1328049v1_genomic.fna/target_genomes.txt --output GCF_013280495.1_ASM1328049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:58,106] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:58,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:58,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:58,115] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:58,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:58,115] [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
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	100.0	1211	1213	95	conclusive
Brevibacterium iodinum	strain=ATCC 49514	GCA_900169265.1	31943	31943	type	True	94.7796	1000	1213	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	94.3798	1054	1213	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	94.3655	1055	1213	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_008868375.1	1703	1703	suspected-type	True	91.6039	995	1213	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_900169165.1	1703	1703	suspected-type	True	91.5819	1007	1213	95	below_threshold
Brevibacterium pigmentatum	strain=YB235	GCA_011617465.1	1496080	1496080	type	True	91.5285	1080	1213	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	81.1202	795	1213	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	80.9658	782	1213	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	78.7967	365	1213	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	78.0036	310	1213	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.7058	122	1213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:58,117] [INFO] DFAST Taxonomy check result was written to GCF_013280495.1_ASM1328049v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:58,117] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:58,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:58,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference/checkm_data
[2024-01-25 18:08:58,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:58,156] [INFO] Task started: CheckM
[2024-01-25 18:08:58,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013280495.1_ASM1328049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013280495.1_ASM1328049v1_genomic.fna/checkm_input GCF_013280495.1_ASM1328049v1_genomic.fna/checkm_result
[2024-01-25 18:09:32,919] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:32,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:32,934] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:32,934] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:32,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013280495.1_ASM1328049v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:32,935] [INFO] Task started: Blastn
[2024-01-25 18:09:32,935] [INFO] Running command: blastn -query GCF_013280495.1_ASM1328049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463fc29a-671a-465c-9b84-92dbfca6749c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013280495.1_ASM1328049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:34,524] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:34,526] [INFO] Selected 7 target genomes.
[2024-01-25 18:09:34,527] [INFO] Target genome list was writen to GCF_013280495.1_ASM1328049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:34,533] [INFO] Task started: fastANI
[2024-01-25 18:09:34,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg64254382-12b5-4b5e-90e0-3cdd661c9462/GCF_013280495.1_ASM1328049v1_genomic.fna.gz --refList GCF_013280495.1_ASM1328049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013280495.1_ASM1328049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:41,420] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:41,425] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:41,425] [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_013280495.1	s__Brevibacterium permense	100.0	1211	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900169265.1	s__Brevibacterium iodinum	94.8	999	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013623905.1	s__Brevibacterium sediminis	94.3655	1055	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_900169165.1	s__Brevibacterium linens	91.5748	1008	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.12	96.02	0.90	0.82	5	-
GCF_011617465.1	s__Brevibacterium sp011617465	91.5311	1079	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844365.1	s__Brevibacterium sp012844365	91.2186	1053	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105315.1	s__Brevibacterium siliguriense	90.1158	1015	1213	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:41,428] [INFO] GTDB search result was written to GCF_013280495.1_ASM1328049v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:41,428] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:41,431] [INFO] DFAST_QC result json was written to GCF_013280495.1_ASM1328049v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:41,431] [INFO] DFAST_QC completed!
[2024-01-25 18:09:41,431] [INFO] Total running time: 0h1m6s