[2024-01-24 13:49:31,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:31,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:31,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference
[2024-01-24 13:49:32,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,253] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c52815f-44bf-48de-ab05-105fbdf9d3bf/GCF_014138045.1_ASM1413804v1_genomic.fna.gz | prodigal -d GCF_014138045.1_ASM1413804v1_genomic.fna/cds.fna -a GCF_014138045.1_ASM1413804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,020] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,020] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,020] [INFO] Running command: hmmsearch --tblout GCF_014138045.1_ASM1413804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference/reference_markers.hmm GCF_014138045.1_ASM1413804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:45,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:45,310] [INFO] Found 6/6 markers.
[2024-01-24 13:49:45,366] [INFO] Query marker FASTA was written to GCF_014138045.1_ASM1413804v1_genomic.fna/markers.fasta
[2024-01-24 13:49:45,367] [INFO] Task started: Blastn
[2024-01-24 13:49:45,367] [INFO] Running command: blastn -query GCF_014138045.1_ASM1413804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference/reference_markers.fasta -out GCF_014138045.1_ASM1413804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,677] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,685] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:46,686] [INFO] Target genome list was writen to GCF_014138045.1_ASM1413804v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:46,697] [INFO] Task started: fastANI
[2024-01-24 13:49:46,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c52815f-44bf-48de-ab05-105fbdf9d3bf/GCF_014138045.1_ASM1413804v1_genomic.fna.gz --refList GCF_014138045.1_ASM1413804v1_genomic.fna/target_genomes.txt --output GCF_014138045.1_ASM1413804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:09,909] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:09,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:09,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:09,931] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:09,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:09,931] [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 ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	100.0	1479	1484	95	conclusive
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	84.6204	992	1484	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	83.9568	923	1484	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	83.1292	850	1484	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	82.8265	836	1484	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	82.8175	810	1484	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	82.7558	844	1484	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	82.645	820	1484	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.5962	811	1484	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.4906	815	1484	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.3127	807	1484	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	81.8434	737	1484	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.8432	740	1484	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	81.6651	762	1484	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	81.5563	720	1484	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	81.4826	661	1484	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	81.466	719	1484	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	81.2933	708	1484	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	81.1931	719	1484	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	81.1534	675	1484	95	below_threshold
Nocardioides piscis	strain=HDW12A	GCA_011300215.1	2714938	2714938	type	True	80.89	678	1484	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.6781	673	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:09,936] [INFO] DFAST Taxonomy check result was written to GCF_014138045.1_ASM1413804v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:09,937] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:09,937] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:09,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference/checkm_data
[2024-01-24 13:50:09,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:09,989] [INFO] Task started: CheckM
[2024-01-24 13:50:09,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138045.1_ASM1413804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138045.1_ASM1413804v1_genomic.fna/checkm_input GCF_014138045.1_ASM1413804v1_genomic.fna/checkm_result
[2024-01-24 13:51:24,928] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:24,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:24,953] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:24,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:24,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138045.1_ASM1413804v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:24,954] [INFO] Task started: Blastn
[2024-01-24 13:51:24,954] [INFO] Running command: blastn -query GCF_014138045.1_ASM1413804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e749449-ec6d-4fd0-b73f-469d4af0e8e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138045.1_ASM1413804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:26,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:27,000] [INFO] Selected 19 target genomes.
[2024-01-24 13:51:27,001] [INFO] Target genome list was writen to GCF_014138045.1_ASM1413804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:27,030] [INFO] Task started: fastANI
[2024-01-24 13:51:27,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c52815f-44bf-48de-ab05-105fbdf9d3bf/GCF_014138045.1_ASM1413804v1_genomic.fna.gz --refList GCF_014138045.1_ASM1413804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138045.1_ASM1413804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:46,228] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:46,243] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:46,243] [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_014138045.1	s__Nocardioides ginsengisegetis	100.0	1481	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	conclusive
GCF_014212315.1	s__Nocardioides luti	84.6021	994	1484	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	83.9227	928	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	83.3256	883	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	83.109	850	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	82.8183	837	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.6854	825	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_015024225.1	s__Nocardioides sp015024225	82.6623	820	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_001425175.1	s__Nocardioides sp001425175	82.6222	906	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013778305.1	s__Nocardioides sp013778305	82.6087	834	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014266025.1	s__Nocardioides deserti	82.5972	811	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011250565.1	s__Nocardioides sp011250565	82.5698	809	1484	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	82.5522	838	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620645.1	s__Nocardioides sp000620645	82.4676	842	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	82.4341	789	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015265.1	s__Nocardioides sp000015265	82.3677	868	1484	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	81.838	738	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633575.1	s__Nocardioides sp003633575	81.6722	771	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	81.5173	721	1484	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 13:51:46,245] [INFO] GTDB search result was written to GCF_014138045.1_ASM1413804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:46,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:46,249] [INFO] DFAST_QC result json was written to GCF_014138045.1_ASM1413804v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:46,249] [INFO] DFAST_QC completed!
[2024-01-24 13:51:46,249] [INFO] Total running time: 0h2m15s