[2024-01-24 13:21:40,648] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:40,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:40,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference
[2024-01-24 13:21:42,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:42,050] [INFO] Task started: Prodigal
[2024-01-24 13:21:42,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b8c6f8d-5eb5-4cf1-905f-886dd626d8ea/GCF_013409425.1_ASM1340942v1_genomic.fna.gz | prodigal -d GCF_013409425.1_ASM1340942v1_genomic.fna/cds.fna -a GCF_013409425.1_ASM1340942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:52,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:52,517] [INFO] Task started: HMMsearch
[2024-01-24 13:21:52,517] [INFO] Running command: hmmsearch --tblout GCF_013409425.1_ASM1340942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference/reference_markers.hmm GCF_013409425.1_ASM1340942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:52,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:52,838] [INFO] Found 6/6 markers.
[2024-01-24 13:21:52,875] [INFO] Query marker FASTA was written to GCF_013409425.1_ASM1340942v1_genomic.fna/markers.fasta
[2024-01-24 13:21:52,875] [INFO] Task started: Blastn
[2024-01-24 13:21:52,875] [INFO] Running command: blastn -query GCF_013409425.1_ASM1340942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference/reference_markers.fasta -out GCF_013409425.1_ASM1340942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:54,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:54,120] [INFO] Selected 24 target genomes.
[2024-01-24 13:21:54,120] [INFO] Target genome list was writen to GCF_013409425.1_ASM1340942v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:54,153] [INFO] Task started: fastANI
[2024-01-24 13:21:54,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b8c6f8d-5eb5-4cf1-905f-886dd626d8ea/GCF_013409425.1_ASM1340942v1_genomic.fna.gz --refList GCF_013409425.1_ASM1340942v1_genomic.fna/target_genomes.txt --output GCF_013409425.1_ASM1340942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:17,763] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:17,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:17,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:17,782] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:17,782] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:17,783] [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 perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	100.0	1204	1204	95	conclusive
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.9773	792	1204	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.5278	731	1204	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.4248	756	1204	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.4042	759	1204	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	81.3924	725	1204	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.1931	744	1204	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	81.1555	686	1204	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.1214	708	1204	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.1006	709	1204	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.0497	743	1204	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.0285	731	1204	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.9899	687	1204	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	80.9151	641	1204	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.8667	671	1204	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.7398	666	1204	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.7029	701	1204	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.6561	635	1204	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.6274	687	1204	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	80.5913	677	1204	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.2497	635	1204	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	80.235	604	1204	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	80.0533	586	1204	95	below_threshold
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	79.9995	578	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:17,790] [INFO] DFAST Taxonomy check result was written to GCF_013409425.1_ASM1340942v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:17,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:17,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:17,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference/checkm_data
[2024-01-24 13:22:17,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:17,830] [INFO] Task started: CheckM
[2024-01-24 13:22:17,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409425.1_ASM1340942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409425.1_ASM1340942v1_genomic.fna/checkm_input GCF_013409425.1_ASM1340942v1_genomic.fna/checkm_result
[2024-01-24 13:23:21,719] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:21,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:21,737] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:21,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:21,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409425.1_ASM1340942v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:21,737] [INFO] Task started: Blastn
[2024-01-24 13:23:21,738] [INFO] Running command: blastn -query GCF_013409425.1_ASM1340942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6580dc8f-a143-4edb-97d4-cc1a5afb0938/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409425.1_ASM1340942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:23,772] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:23,775] [INFO] Selected 24 target genomes.
[2024-01-24 13:23:23,775] [INFO] Target genome list was writen to GCF_013409425.1_ASM1340942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:23,785] [INFO] Task started: fastANI
[2024-01-24 13:23:23,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b8c6f8d-5eb5-4cf1-905f-886dd626d8ea/GCF_013409425.1_ASM1340942v1_genomic.fna.gz --refList GCF_013409425.1_ASM1340942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409425.1_ASM1340942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:46,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:46,084] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:46,084] [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_013409425.1	s__Nocardioides perillae	100.0	1204	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015070375.1	s__Nocardioides kribbensis	81.9919	791	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_011250565.1	s__Nocardioides sp011250565	81.6926	736	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701885.1	s__Nocardioides sp009701885	81.6524	708	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	81.5356	730	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014266025.1	s__Nocardioides deserti	81.4571	753	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013177455.1	s__Nocardioides sp013177455	81.4458	760	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013408145.1	s__Nocardioides marinus	81.3851	723	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_001627335.1	s__Nocardioides sp001627335	81.3106	658	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCA_902805925.1	s__Nocardioides sp902805925	81.2079	573	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	81.1477	700	1204	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	81.1146	709	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	81.0511	711	1204	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	81.0054	721	1204	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	80.9944	699	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	80.677	703	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	80.6447	672	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	80.6374	710	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004564375.1	s__Nocardioides euryhalodurans	80.5985	689	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620705.1	s__Nocardioides sp000620705	80.5733	686	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424755.1	s__Marmoricola sp001424755	80.5405	670	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865585.1	s__Nocardioides houyundeii	80.1805	606	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_001552535.1	s__Nocardioides jensenii	80.0523	587	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646375.1	s__Nocardioides phosphati	79.9817	580	1204	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 13:23:46,086] [INFO] GTDB search result was written to GCF_013409425.1_ASM1340942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:46,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:46,096] [INFO] DFAST_QC result json was written to GCF_013409425.1_ASM1340942v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:46,096] [INFO] DFAST_QC completed!
[2024-01-24 13:23:46,096] [INFO] Total running time: 0h2m5s