[2024-01-25 17:41:50,546] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:50,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:50,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference
[2024-01-25 17:41:51,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:51,640] [INFO] Task started: Prodigal
[2024-01-25 17:41:51,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg253a00b7-9ca1-4c26-b1a6-3c239a5c2f04/GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna.gz | prodigal -d GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/cds.fna -a GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:59,734] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:59,735] [INFO] Task started: HMMsearch
[2024-01-25 17:41:59,735] [INFO] Running command: hmmsearch --tblout GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference/reference_markers.hmm GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:59,918] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:59,919] [INFO] Found 6/6 markers.
[2024-01-25 17:41:59,941] [INFO] Query marker FASTA was written to GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/markers.fasta
[2024-01-25 17:41:59,942] [INFO] Task started: Blastn
[2024-01-25 17:41:59,942] [INFO] Running command: blastn -query GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/markers.fasta -db /var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference/reference_markers.fasta -out GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:00,743] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:00,750] [INFO] Selected 19 target genomes.
[2024-01-25 17:42:00,750] [INFO] Target genome list was writen to GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/target_genomes.txt
[2024-01-25 17:42:00,758] [INFO] Task started: fastANI
[2024-01-25 17:42:00,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg253a00b7-9ca1-4c26-b1a6-3c239a5c2f04/GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna.gz --refList GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/target_genomes.txt --output GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:12,862] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:12,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:12,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:12,873] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:12,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:12,873] [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
Devriesea agamarum	strain=IMP2	GCA_900070355.1	472569	472569	type	True	100.0	986	986	95	conclusive
Brachybacterium massiliense	strain=mt5	GCA_900184245.1	1755098	1755098	type	True	78.1498	100	986	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	78.1203	100	986	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	77.9113	104	986	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	77.9095	103	986	95	below_threshold
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	77.7358	103	986	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	77.6847	109	986	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	77.6473	99	986	95	below_threshold
Brachybacterium timonense	strain=Marseille-P4339	GCA_900258505.1	2050896	2050896	type	True	77.6402	97	986	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	77.593	101	986	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	77.5704	90	986	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	77.5471	96	986	95	below_threshold
Brachybacterium endophyticum	strain=M1HQ-2	GCA_003130585.1	2182385	2182385	type	True	77.5271	93	986	95	below_threshold
Brachybacterium avium	strain=VR2415	GCA_002216795.1	2017485	2017485	type	True	77.3007	104	986	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	77.2659	106	986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:12,874] [INFO] DFAST Taxonomy check result was written to GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/tc_result.tsv
[2024-01-25 17:42:12,875] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:12,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:12,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference/checkm_data
[2024-01-25 17:42:12,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:12,907] [INFO] Task started: CheckM
[2024-01-25 17:42:12,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/checkm_input GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/checkm_result
[2024-01-25 17:42:40,007] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:40,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:40,025] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:40,025] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:40,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/markers.fasta)
[2024-01-25 17:42:40,026] [INFO] Task started: Blastn
[2024-01-25 17:42:40,026] [INFO] Running command: blastn -query GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/markers.fasta -db /var/lib/cwl/stg6122882a-acbc-490a-9890-eeb0f650eb29/dqc_reference/reference_markers_gtdb.fasta -out GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:41,254] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:41,257] [INFO] Selected 19 target genomes.
[2024-01-25 17:42:41,257] [INFO] Target genome list was writen to GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:41,268] [INFO] Task started: fastANI
[2024-01-25 17:42:41,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg253a00b7-9ca1-4c26-b1a6-3c239a5c2f04/GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna.gz --refList GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/target_genomes_gtdb.txt --output GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:53,006] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:53,018] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:53,018] [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_900070355.1	s__Devriesea agamarum	100.0	985	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Devriesea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019218375.1	s__TAE3-ERU5 sp019218375	78.8022	87	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__TAE3-ERU5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218415.1	s__TAE3-ERU5 sp019218415	78.3957	93	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__TAE3-ERU5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184245.1	s__Brachybacterium massiliense	77.9746	99	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204755.1	s__Brachybacterium aquaticum	77.7685	103	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002332425.1	s__Brachybacterium alimentarium	77.756	92	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.24	99.17	0.94	0.92	9	-
GCF_000576425.1	s__Brachybacterium phenoliresistens	77.7478	104	986	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	77.735	102	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209585.1	s__Brachybacterium sp015209585	77.6847	109	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258505.1	s__Brachybacterium timonense	77.6402	97	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871795.1	s__Brachybacterium sp002871795	77.6301	98	986	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	77.5471	96	986	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	77.5431	90	986	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	77.5271	93	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216795.1	s__Brachybacterium avium	77.4675	105	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994255.1	s__Brachybacterium paraconglomeratum	77.3709	93	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	96.80	96.03	0.88	0.86	7	-
GCF_003711805.1	s__Brachybacterium intestinipullorum	76.9285	104	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.17	99.17	0.95	0.95	2	-
GCA_019118275.1	s__Brachybacterium merdavium	76.6898	82	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:53,020] [INFO] GTDB search result was written to GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:53,020] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:53,024] [INFO] DFAST_QC result json was written to GCF_900070355.1_S2_rcS3_S1_rcS3_genomic.fna/dqc_result.json
[2024-01-25 17:42:53,024] [INFO] DFAST_QC completed!
[2024-01-25 17:42:53,024] [INFO] Total running time: 0h1m2s