[2024-01-24 11:22:49,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference
[2024-01-24 11:22:50,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,741] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,741] [INFO] Running command: gunzip -c /var/lib/cwl/stge6f4deae-42cf-44a2-ae20-e3f3e648c11f/GCF_025999835.1_ASM2599983v1_genomic.fna.gz | prodigal -d GCF_025999835.1_ASM2599983v1_genomic.fna/cds.fna -a GCF_025999835.1_ASM2599983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:00,953] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:00,953] [INFO] Task started: HMMsearch
[2024-01-24 11:23:00,953] [INFO] Running command: hmmsearch --tblout GCF_025999835.1_ASM2599983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference/reference_markers.hmm GCF_025999835.1_ASM2599983v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:01,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:01,210] [INFO] Found 6/6 markers.
[2024-01-24 11:23:01,244] [INFO] Query marker FASTA was written to GCF_025999835.1_ASM2599983v1_genomic.fna/markers.fasta
[2024-01-24 11:23:01,245] [INFO] Task started: Blastn
[2024-01-24 11:23:01,245] [INFO] Running command: blastn -query GCF_025999835.1_ASM2599983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference/reference_markers.fasta -out GCF_025999835.1_ASM2599983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:01,906] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:01,909] [INFO] Selected 25 target genomes.
[2024-01-24 11:23:01,910] [INFO] Target genome list was writen to GCF_025999835.1_ASM2599983v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:01,919] [INFO] Task started: fastANI
[2024-01-24 11:23:01,920] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f4deae-42cf-44a2-ae20-e3f3e648c11f/GCF_025999835.1_ASM2599983v1_genomic.fna.gz --refList GCF_025999835.1_ASM2599983v1_genomic.fna/target_genomes.txt --output GCF_025999835.1_ASM2599983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:19,089] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:19,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:19,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:19,108] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:23:19,108] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:23:19,108] [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
Symbiobacterium thermophilum	strain=IAM14863	GCA_000009905.1	2734	2734	type	True	77.041	216	1199	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	76.8211	210	1199	95	below_threshold
Calditerricola satsumensis	strain=JCM 14719	GCA_014646935.1	373054	373054	type	True	76.3535	59	1199	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	76.2514	157	1199	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	75.4048	89	1199	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.2529	65	1199	95	below_threshold
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.2058	68	1199	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	75.1588	54	1199	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	75.1572	83	1199	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	75.1066	80	1199	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.0332	173	1199	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	74.9855	74	1199	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.9788	173	1199	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	74.9346	94	1199	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.9067	138	1199	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	74.8488	102	1199	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	74.7946	63	1199	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	74.6814	202	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:19,111] [INFO] DFAST Taxonomy check result was written to GCF_025999835.1_ASM2599983v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:19,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:19,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:19,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference/checkm_data
[2024-01-24 11:23:19,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:19,151] [INFO] Task started: CheckM
[2024-01-24 11:23:19,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025999835.1_ASM2599983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025999835.1_ASM2599983v1_genomic.fna/checkm_input GCF_025999835.1_ASM2599983v1_genomic.fna/checkm_result
[2024-01-24 11:23:55,655] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:55,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:55,677] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:55,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:55,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025999835.1_ASM2599983v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:55,679] [INFO] Task started: Blastn
[2024-01-24 11:23:55,679] [INFO] Running command: blastn -query GCF_025999835.1_ASM2599983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8572447d-4f04-4d95-b30b-20aa5a3cb816/dqc_reference/reference_markers_gtdb.fasta -out GCF_025999835.1_ASM2599983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:56,728] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:56,733] [INFO] Selected 27 target genomes.
[2024-01-24 11:23:56,733] [INFO] Target genome list was writen to GCF_025999835.1_ASM2599983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:56,774] [INFO] Task started: fastANI
[2024-01-24 11:23:56,774] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f4deae-42cf-44a2-ae20-e3f3e648c11f/GCF_025999835.1_ASM2599983v1_genomic.fna.gz --refList GCF_025999835.1_ASM2599983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025999835.1_ASM2599983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:11,320] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:11,335] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:24:11,336] [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
GCA_003242505.1	s__ZC4RG38 sp003242505	77.4731	221	1199	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__ZC4RG38;g__ZC4RG38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009905.1	s__Symbiobacterium thermophilum	77.144	214	1199	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242675.1	s__Symbiobacterium sp003242675	77.1227	193	1199	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874315.1	s__Symbiobacterium terraclitae	76.8221	208	1199	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634385.1	s__Thermaerobacter sp004634385	76.5617	151	1199	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646935.1	s__Calditerricola satsumensis	76.3535	59	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Calditerricolales;f__Calditerricolaceae;g__Calditerricola	95.0	99.92	99.92	0.99	0.99	2	-
GCA_014896375.1	s__Bu92 sp014896375	76.0529	105	1199	d__Bacteria;p__Firmicutes_E;c__RBS10-35;o__RBS10-35;f__Bu92;g__Bu92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055945.1	s__SpSt-190 sp011055945	75.4209	145	1199	d__Bacteria;p__CSP1-3;c__CSP1-3;o__CSP1-3;f__CSP1-3;g__SpSt-190	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	75.2549	65	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873475.1	s__VGXI01 sp016873475	75.2156	65	1199	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__JACNKJ01;f__JACNKJ01;g__VGXI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075165.1	s__JAEUPI01 sp015075165	75.0721	69	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAEUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	74.9155	84	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_016209635.1	s__JACQWC01 sp016209635	74.8739	90	1199	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__JACQWC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125125.1	s__SLDT01 sp007125125	74.8169	52	1199	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLDT01	95.0	99.72	99.72	0.92	0.92	2	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	74.733	55	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:11,337] [INFO] GTDB search result was written to GCF_025999835.1_ASM2599983v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:11,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:11,342] [INFO] DFAST_QC result json was written to GCF_025999835.1_ASM2599983v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:11,342] [INFO] DFAST_QC completed!
[2024-01-24 11:24:11,342] [INFO] Total running time: 0h1m22s