[2024-01-24 15:18:51,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,893] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference
[2024-01-24 15:18:54,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,592] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,593] [INFO] Running command: gunzip -c /var/lib/cwl/stgc889b183-8cbf-49ee-805d-d2c184952029/GCF_013408525.1_ASM1340852v1_genomic.fna.gz | prodigal -d GCF_013408525.1_ASM1340852v1_genomic.fna/cds.fna -a GCF_013408525.1_ASM1340852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:09,232] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:09,232] [INFO] Task started: HMMsearch
[2024-01-24 15:19:09,233] [INFO] Running command: hmmsearch --tblout GCF_013408525.1_ASM1340852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference/reference_markers.hmm GCF_013408525.1_ASM1340852v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:09,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:09,546] [INFO] Found 6/6 markers.
[2024-01-24 15:19:09,591] [INFO] Query marker FASTA was written to GCF_013408525.1_ASM1340852v1_genomic.fna/markers.fasta
[2024-01-24 15:19:09,592] [INFO] Task started: Blastn
[2024-01-24 15:19:09,592] [INFO] Running command: blastn -query GCF_013408525.1_ASM1340852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference/reference_markers.fasta -out GCF_013408525.1_ASM1340852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:11,014] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:11,017] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:11,017] [INFO] Target genome list was writen to GCF_013408525.1_ASM1340852v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:11,513] [INFO] Task started: fastANI
[2024-01-24 15:19:11,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgc889b183-8cbf-49ee-805d-d2c184952029/GCF_013408525.1_ASM1340852v1_genomic.fna.gz --refList GCF_013408525.1_ASM1340852v1_genomic.fna/target_genomes.txt --output GCF_013408525.1_ASM1340852v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:28,862] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:28,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:28,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:28,880] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:28,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:28,881] [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
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	100.0	1750	1751	95	conclusive
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	85.4417	1217	1751	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	85.2537	1082	1751	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	84.9879	1186	1751	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	84.9451	1167	1751	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	84.9001	1178	1751	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	84.8841	1148	1751	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	84.6057	1038	1751	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	84.4597	1093	1751	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.6386	871	1751	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.2887	830	1751	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.1819	732	1751	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.8137	614	1751	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,883] [INFO] DFAST Taxonomy check result was written to GCF_013408525.1_ASM1340852v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:28,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:28,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:28,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference/checkm_data
[2024-01-24 15:19:28,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:28,939] [INFO] Task started: CheckM
[2024-01-24 15:19:28,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408525.1_ASM1340852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408525.1_ASM1340852v1_genomic.fna/checkm_input GCF_013408525.1_ASM1340852v1_genomic.fna/checkm_result
[2024-01-24 15:20:47,017] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:47,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:47,042] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:47,042] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:47,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408525.1_ASM1340852v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:47,043] [INFO] Task started: Blastn
[2024-01-24 15:20:47,043] [INFO] Running command: blastn -query GCF_013408525.1_ASM1340852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3632fea-ff51-4661-996f-b11a6ccb56ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408525.1_ASM1340852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:49,095] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:49,099] [INFO] Selected 9 target genomes.
[2024-01-24 15:20:49,099] [INFO] Target genome list was writen to GCF_013408525.1_ASM1340852v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:49,152] [INFO] Task started: fastANI
[2024-01-24 15:20:49,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgc889b183-8cbf-49ee-805d-d2c184952029/GCF_013408525.1_ASM1340852v1_genomic.fna.gz --refList GCF_013408525.1_ASM1340852v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408525.1_ASM1340852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:02,578] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:02,590] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:02,591] [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_013408525.1	s__Nocardioides aromaticivorans	100.0	1750	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	conclusive
GCF_014873635.1	s__Nocardioides sp014873635	92.7484	1393	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054165.1	s__Nocardioides sp003054165	90.895	1359	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428825.1	s__Nocardioides sp001428825	87.3218	1267	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000519005.1	s__Nocardioides sp000519005	86.4466	1144	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_016803235.1	s__Nocardioides simplex_A	85.6707	1169	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409625.1	s__Nocardioides kongjuensis	85.4357	1220	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192965.1	s__Nocardioides daeguensis	85.2709	1080	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	84.9942	1183	1751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:02,593] [INFO] GTDB search result was written to GCF_013408525.1_ASM1340852v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:02,593] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:02,596] [INFO] DFAST_QC result json was written to GCF_013408525.1_ASM1340852v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:02,597] [INFO] DFAST_QC completed!
[2024-01-24 15:21:02,597] [INFO] Total running time: 0h2m11s