[2024-01-25 19:57:05,711] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference
[2024-01-25 19:57:06,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,877] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg79eda377-63dd-4eed-8ddf-7bedc28e15c9/GCF_013409965.1_ASM1340996v1_genomic.fna.gz | prodigal -d GCF_013409965.1_ASM1340996v1_genomic.fna/cds.fna -a GCF_013409965.1_ASM1340996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:17,331] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:17,331] [INFO] Task started: HMMsearch
[2024-01-25 19:57:17,331] [INFO] Running command: hmmsearch --tblout GCF_013409965.1_ASM1340996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference/reference_markers.hmm GCF_013409965.1_ASM1340996v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:17,572] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:17,573] [INFO] Found 6/6 markers.
[2024-01-25 19:57:17,607] [INFO] Query marker FASTA was written to GCF_013409965.1_ASM1340996v1_genomic.fna/markers.fasta
[2024-01-25 19:57:17,608] [INFO] Task started: Blastn
[2024-01-25 19:57:17,608] [INFO] Running command: blastn -query GCF_013409965.1_ASM1340996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference/reference_markers.fasta -out GCF_013409965.1_ASM1340996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:18,787] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:18,791] [INFO] Selected 10 target genomes.
[2024-01-25 19:57:18,791] [INFO] Target genome list was writen to GCF_013409965.1_ASM1340996v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:18,796] [INFO] Task started: fastANI
[2024-01-25 19:57:18,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg79eda377-63dd-4eed-8ddf-7bedc28e15c9/GCF_013409965.1_ASM1340996v1_genomic.fna.gz --refList GCF_013409965.1_ASM1340996v1_genomic.fna/target_genomes.txt --output GCF_013409965.1_ASM1340996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:30,665] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:30,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:30,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:30,673] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:57:30,673] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:30,673] [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 marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	100.0	1392	1393	95	conclusive
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	99.988	1389	1393	95	conclusive
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	90.4601	1171	1393	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	90.4481	1157	1393	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	90.4335	1155	1393	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	81.1264	723	1393	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.8901	723	1393	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.6137	700	1393	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.3263	707	1393	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.3196	765	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:30,675] [INFO] DFAST Taxonomy check result was written to GCF_013409965.1_ASM1340996v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:30,678] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:30,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:30,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference/checkm_data
[2024-01-25 19:57:30,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:30,719] [INFO] Task started: CheckM
[2024-01-25 19:57:30,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409965.1_ASM1340996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409965.1_ASM1340996v1_genomic.fna/checkm_input GCF_013409965.1_ASM1340996v1_genomic.fna/checkm_result
[2024-01-25 19:58:39,356] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:39,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:39,385] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:39,385] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:39,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409965.1_ASM1340996v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:39,386] [INFO] Task started: Blastn
[2024-01-25 19:58:39,386] [INFO] Running command: blastn -query GCF_013409965.1_ASM1340996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0c41912-e30f-4140-99d5-8d0b74583166/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409965.1_ASM1340996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:41,367] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:41,370] [INFO] Selected 19 target genomes.
[2024-01-25 19:58:41,370] [INFO] Target genome list was writen to GCF_013409965.1_ASM1340996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:41,394] [INFO] Task started: fastANI
[2024-01-25 19:58:41,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg79eda377-63dd-4eed-8ddf-7bedc28e15c9/GCF_013409965.1_ASM1340996v1_genomic.fna.gz --refList GCF_013409965.1_ASM1340996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409965.1_ASM1340996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:02,377] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:02,389] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:02,389] [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_013466785.1	s__Nocardioides marinisabuli	99.988	1389	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_016907435.1	s__Nocardioides salarius	90.4601	1171	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001653335.1	s__Nocardioides dokdonensis	87.379	1102	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	83.4278	862	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013408145.1	s__Nocardioides marinus	83.2994	900	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_014127485.1	s__Nocardioides sp014127485	82.5863	836	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.39	878	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013155365.1	s__Nocardioides sp013155365	82.3063	812	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011420305.2	s__Nocardioides sp011420305	82.1756	793	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003660455.1	s__Nocardioides ferulae	82.0932	857	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	82.0704	793	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018459925.1	s__Nocardioides aquaticus	81.5847	797	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506435.1	s__Nocardioides sp902506435	81.5706	770	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429625.1	s__Nocardioides sp001429625	81.5148	766	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319165.1	s__Nocardioides acrostichi	81.4081	793	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	81.2772	758	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	80.8986	722	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.8324	699	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785795.1	s__Nocardioides eburneiflavus	80.6738	756	1393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:02,390] [INFO] GTDB search result was written to GCF_013409965.1_ASM1340996v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:02,391] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:02,395] [INFO] DFAST_QC result json was written to GCF_013409965.1_ASM1340996v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:02,397] [INFO] DFAST_QC completed!
[2024-01-25 19:59:02,397] [INFO] Total running time: 0h1m57s