[2024-01-24 14:14:20,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference
[2024-01-24 14:14:21,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,835] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg045556c7-e2b3-4986-b818-6fbff1492c64/GCF_013408415.1_ASM1340841v1_genomic.fna.gz | prodigal -d GCF_013408415.1_ASM1340841v1_genomic.fna/cds.fna -a GCF_013408415.1_ASM1340841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:33,504] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:33,504] [INFO] Task started: HMMsearch
[2024-01-24 14:14:33,504] [INFO] Running command: hmmsearch --tblout GCF_013408415.1_ASM1340841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference/reference_markers.hmm GCF_013408415.1_ASM1340841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,754] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,786] [INFO] Query marker FASTA was written to GCF_013408415.1_ASM1340841v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,787] [INFO] Task started: Blastn
[2024-01-24 14:14:33,787] [INFO] Running command: blastn -query GCF_013408415.1_ASM1340841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference/reference_markers.fasta -out GCF_013408415.1_ASM1340841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:35,010] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:35,014] [INFO] Selected 23 target genomes.
[2024-01-24 14:14:35,014] [INFO] Target genome list was writen to GCF_013408415.1_ASM1340841v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:35,030] [INFO] Task started: fastANI
[2024-01-24 14:14:35,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg045556c7-e2b3-4986-b818-6fbff1492c64/GCF_013408415.1_ASM1340841v1_genomic.fna.gz --refList GCF_013408415.1_ASM1340841v1_genomic.fna/target_genomes.txt --output GCF_013408415.1_ASM1340841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:55,368] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:55,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:55,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:55,387] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:55,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:55,387] [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 daedukensis	strain=DSM 23819	GCA_013408415.1	634462	634462	type	True	100.0	1269	1269	95	conclusive
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	82.0176	757	1269	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.4387	642	1269	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.2407	581	1269	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.2281	628	1269	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.1054	623	1269	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.0932	572	1269	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.0509	596	1269	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.0279	555	1269	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.9711	585	1269	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.9133	592	1269	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.8957	550	1269	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	79.8687	482	1269	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	79.7949	586	1269	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.7879	632	1269	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	79.7656	544	1269	95	below_threshold
Nocardioides alcanivorans	strain=NGK65	GCA_021555175.1	2897352	2897352	type	True	79.6989	598	1269	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	79.5447	576	1269	95	below_threshold
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	79.5405	490	1269	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.3968	567	1269	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	79.2105	544	1269	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	79.1049	516	1269	95	below_threshold
Nocardioides agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	78.9814	470	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:55,389] [INFO] DFAST Taxonomy check result was written to GCF_013408415.1_ASM1340841v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:55,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:55,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:55,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference/checkm_data
[2024-01-24 14:14:55,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:55,430] [INFO] Task started: CheckM
[2024-01-24 14:14:55,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408415.1_ASM1340841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408415.1_ASM1340841v1_genomic.fna/checkm_input GCF_013408415.1_ASM1340841v1_genomic.fna/checkm_result
[2024-01-24 14:16:06,566] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:06,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:06,586] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:06,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:06,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408415.1_ASM1340841v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:06,587] [INFO] Task started: Blastn
[2024-01-24 14:16:06,587] [INFO] Running command: blastn -query GCF_013408415.1_ASM1340841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1dfe500-04eb-4826-ad13-8bff0e78294b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408415.1_ASM1340841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:08,372] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:08,376] [INFO] Selected 13 target genomes.
[2024-01-24 14:16:08,376] [INFO] Target genome list was writen to GCF_013408415.1_ASM1340841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:08,388] [INFO] Task started: fastANI
[2024-01-24 14:16:08,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg045556c7-e2b3-4986-b818-6fbff1492c64/GCF_013408415.1_ASM1340841v1_genomic.fna.gz --refList GCF_013408415.1_ASM1340841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408415.1_ASM1340841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:21,106] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:21,118] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:21,119] [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_013408415.1	s__Nocardioides daedukensis	100.0	1269	1269	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	82.0439	811	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_001552535.1	s__Nocardioides jensenii	82.0153	758	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272695.1	s__Nocardioides sp012272695	82.015	764	1269	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	81.6427	778	1269	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	80.4762	641	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.141	619	1269	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	79.9028	594	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015024225.1	s__Nocardioides sp015024225	79.7697	591	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_000620705.1	s__Nocardioides sp000620705	79.6928	595	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	79.6625	568	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_006346315.1	s__Nocardioides litoris	79.5797	572	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352455.1	s__Nocardioides islandensis	79.1009	516	1269	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 14:16:21,121] [INFO] GTDB search result was written to GCF_013408415.1_ASM1340841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:21,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:21,126] [INFO] DFAST_QC result json was written to GCF_013408415.1_ASM1340841v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:21,126] [INFO] DFAST_QC completed!
[2024-01-24 14:16:21,126] [INFO] Total running time: 0h2m1s