[2024-01-24 14:22:01,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference
[2024-01-24 14:22:02,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,972] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,972] [INFO] Running command: gunzip -c /var/lib/cwl/stg78a18805-aa2d-4110-8b47-4e2e0fc0735d/GCF_001552535.1_ASM155253v1_genomic.fna.gz | prodigal -d GCF_001552535.1_ASM155253v1_genomic.fna/cds.fna -a GCF_001552535.1_ASM155253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:18,068] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:18,069] [INFO] Task started: HMMsearch
[2024-01-24 14:22:18,069] [INFO] Running command: hmmsearch --tblout GCF_001552535.1_ASM155253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference/reference_markers.hmm GCF_001552535.1_ASM155253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:18,357] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:18,358] [INFO] Found 6/6 markers.
[2024-01-24 14:22:18,406] [INFO] Query marker FASTA was written to GCF_001552535.1_ASM155253v1_genomic.fna/markers.fasta
[2024-01-24 14:22:18,406] [INFO] Task started: Blastn
[2024-01-24 14:22:18,407] [INFO] Running command: blastn -query GCF_001552535.1_ASM155253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference/reference_markers.fasta -out GCF_001552535.1_ASM155253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:19,657] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:19,660] [INFO] Selected 24 target genomes.
[2024-01-24 14:22:19,661] [INFO] Target genome list was writen to GCF_001552535.1_ASM155253v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:19,674] [INFO] Task started: fastANI
[2024-01-24 14:22:19,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a18805-aa2d-4110-8b47-4e2e0fc0735d/GCF_001552535.1_ASM155253v1_genomic.fna.gz --refList GCF_001552535.1_ASM155253v1_genomic.fna/target_genomes.txt --output GCF_001552535.1_ASM155253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:41,991] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:41,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:41,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:42,011] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:42,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:42,011] [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 jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	100.0	1596	1607	95	conclusive
Nocardioides daedukensis	strain=DSM 23819	GCA_013408415.1	634462	634462	type	True	81.9003	781	1607	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.8268	726	1607	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.6975	679	1607	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.5086	655	1607	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.3914	658	1607	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.3912	650	1607	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.3628	698	1607	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	80.2879	643	1607	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	80.201	653	1607	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.1739	626	1607	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	80.17	528	1607	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	80.1037	661	1607	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.0811	652	1607	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	80.0147	645	1607	95	below_threshold
Nocardioides alcanivorans	strain=NGK65	GCA_021555175.1	2897352	2897352	type	True	79.9866	643	1607	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	79.9792	645	1607	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	79.9789	651	1607	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.9601	635	1607	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.9492	648	1607	95	below_threshold
Nocardioides jejuensis	strain=18JY15-6	GCA_004337475.1	2502782	2502782	type	True	79.7013	489	1607	95	below_threshold
Nocardioides speluncae	strain=YIM ART13	GCA_003121585.1	2670337	2670337	type	True	79.6948	698	1607	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	79.689	585	1607	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.488	595	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:42,013] [INFO] DFAST Taxonomy check result was written to GCF_001552535.1_ASM155253v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:42,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:42,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:42,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference/checkm_data
[2024-01-24 14:22:42,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:42,065] [INFO] Task started: CheckM
[2024-01-24 14:22:42,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552535.1_ASM155253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552535.1_ASM155253v1_genomic.fna/checkm_input GCF_001552535.1_ASM155253v1_genomic.fna/checkm_result
[2024-01-24 14:24:05,783] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:05,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:05,809] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:05,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:05,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552535.1_ASM155253v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:05,810] [INFO] Task started: Blastn
[2024-01-24 14:24:05,810] [INFO] Running command: blastn -query GCF_001552535.1_ASM155253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aab315a-da89-43b7-a472-796e45b827b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552535.1_ASM155253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:07,583] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:07,586] [INFO] Selected 8 target genomes.
[2024-01-24 14:24:07,587] [INFO] Target genome list was writen to GCF_001552535.1_ASM155253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:07,594] [INFO] Task started: fastANI
[2024-01-24 14:24:07,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a18805-aa2d-4110-8b47-4e2e0fc0735d/GCF_001552535.1_ASM155253v1_genomic.fna.gz --refList GCF_001552535.1_ASM155253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552535.1_ASM155253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:15,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:15,111] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:15,111] [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_001552535.1	s__Nocardioides jensenii	100.0	1596	1607	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_001426745.1	s__Nocardioides sp001426745	87.1019	1163	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_012272695.1	s__Nocardioides sp012272695	83.6714	929	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429555.1	s__Nocardioides sp001429555	83.5962	980	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408415.1	s__Nocardioides daedukensis	81.9003	781	1607	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	80.5267	653	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	80.2971	512	1607	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	80.2965	642	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:15,113] [INFO] GTDB search result was written to GCF_001552535.1_ASM155253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:15,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:15,117] [INFO] DFAST_QC result json was written to GCF_001552535.1_ASM155253v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:15,117] [INFO] DFAST_QC completed!
[2024-01-24 14:24:15,117] [INFO] Total running time: 0h2m13s