[2024-01-24 13:12:55,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference
[2024-01-24 13:12:57,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,257] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg8250e7f3-f622-4d20-9523-0cbe11c63022/GCF_013410375.1_ASM1341037v1_genomic.fna.gz | prodigal -d GCF_013410375.1_ASM1341037v1_genomic.fna/cds.fna -a GCF_013410375.1_ASM1341037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:09,456] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:09,456] [INFO] Task started: HMMsearch
[2024-01-24 13:13:09,456] [INFO] Running command: hmmsearch --tblout GCF_013410375.1_ASM1341037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference/reference_markers.hmm GCF_013410375.1_ASM1341037v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:09,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:09,748] [INFO] Found 6/6 markers.
[2024-01-24 13:13:09,789] [INFO] Query marker FASTA was written to GCF_013410375.1_ASM1341037v1_genomic.fna/markers.fasta
[2024-01-24 13:13:09,790] [INFO] Task started: Blastn
[2024-01-24 13:13:09,790] [INFO] Running command: blastn -query GCF_013410375.1_ASM1341037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference/reference_markers.fasta -out GCF_013410375.1_ASM1341037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:11,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:11,215] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:11,216] [INFO] Target genome list was writen to GCF_013410375.1_ASM1341037v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:11,225] [INFO] Task started: fastANI
[2024-01-24 13:13:11,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg8250e7f3-f622-4d20-9523-0cbe11c63022/GCF_013410375.1_ASM1341037v1_genomic.fna.gz --refList GCF_013410375.1_ASM1341037v1_genomic.fna/target_genomes.txt --output GCF_013410375.1_ASM1341037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:21,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:21,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:21,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:21,357] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:21,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:21,358] [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
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	100.0	1472	1472	95	conclusive
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	84.4397	624	1472	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	84.1227	897	1472	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	83.7122	881	1472	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	83.4479	839	1472	95	below_threshold
Leifsonia xyli subsp. cynodontis	strain=DSM 46306	GCA_000470775.1	31966	1575	type	True	82.1988	578	1472	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.4985	556	1472	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	79.2565	465	1472	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.1049	528	1472	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.7715	515	1472	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	78.3599	421	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:21,360] [INFO] DFAST Taxonomy check result was written to GCF_013410375.1_ASM1341037v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:21,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:21,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:21,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference/checkm_data
[2024-01-24 13:13:21,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:21,409] [INFO] Task started: CheckM
[2024-01-24 13:13:21,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410375.1_ASM1341037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410375.1_ASM1341037v1_genomic.fna/checkm_input GCF_013410375.1_ASM1341037v1_genomic.fna/checkm_result
[2024-01-24 13:14:16,735] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:16,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:16,757] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:16,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:16,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410375.1_ASM1341037v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:16,758] [INFO] Task started: Blastn
[2024-01-24 13:14:16,758] [INFO] Running command: blastn -query GCF_013410375.1_ASM1341037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba156e1-8a69-40b0-8b95-58fb40b0ff87/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410375.1_ASM1341037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:19,205] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:19,208] [INFO] Selected 9 target genomes.
[2024-01-24 13:14:19,208] [INFO] Target genome list was writen to GCF_013410375.1_ASM1341037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:19,214] [INFO] Task started: fastANI
[2024-01-24 13:14:19,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg8250e7f3-f622-4d20-9523-0cbe11c63022/GCF_013410375.1_ASM1341037v1_genomic.fna.gz --refList GCF_013410375.1_ASM1341037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410375.1_ASM1341037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:29,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:29,139] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:29,139] [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_013410375.1	s__Leifsonia shinshuensis	100.0	1472	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014217625.1	s__Leifsonia shinshuensis_A	89.86	1138	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565305.1	s__Leifsonia sp017565305	86.609	1102	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	97.25	97.25	0.89	0.89	2	-
GCF_001423695.1	s__Leifsonia sp001423695	86.4155	1047	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898805.1	s__Leifsonia sp001898805	83.9741	887	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359685.1	s__Leifsonia sp013359685	83.9257	863	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003367665.1	s__Leifsonia sp003367665	83.917	885	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647635.1	s__Leifsonia xyli_A	83.8843	870	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633535.1	s__Leifsonia aquatica_A	83.211	888	1472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:29,141] [INFO] GTDB search result was written to GCF_013410375.1_ASM1341037v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:29,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:29,145] [INFO] DFAST_QC result json was written to GCF_013410375.1_ASM1341037v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:29,145] [INFO] DFAST_QC completed!
[2024-01-24 13:14:29,145] [INFO] Total running time: 0h1m33s