[2024-01-24 13:40:43,946] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference
[2024-01-24 13:40:45,368] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,369] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,369] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2c47d50-80d8-4f63-863c-52d0a20efae3/GCF_006346315.1_ASM634631v1_genomic.fna.gz | prodigal -d GCF_006346315.1_ASM634631v1_genomic.fna/cds.fna -a GCF_006346315.1_ASM634631v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,615] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,615] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,616] [INFO] Running command: hmmsearch --tblout GCF_006346315.1_ASM634631v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference/reference_markers.hmm GCF_006346315.1_ASM634631v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,918] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,966] [INFO] Query marker FASTA was written to GCF_006346315.1_ASM634631v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,967] [INFO] Task started: Blastn
[2024-01-24 13:40:58,967] [INFO] Running command: blastn -query GCF_006346315.1_ASM634631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference/reference_markers.fasta -out GCF_006346315.1_ASM634631v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:00,467] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:00,471] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:00,471] [INFO] Target genome list was writen to GCF_006346315.1_ASM634631v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,477] [INFO] Task started: fastANI
[2024-01-24 13:41:00,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c47d50-80d8-4f63-863c-52d0a20efae3/GCF_006346315.1_ASM634631v1_genomic.fna.gz --refList GCF_006346315.1_ASM634631v1_genomic.fna/target_genomes.txt --output GCF_006346315.1_ASM634631v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,618] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,635] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:22,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:22,635] [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 litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	100.0	1541	1541	95	conclusive
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	84.1889	1059	1541	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	83.9053	1039	1541	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.7404	861	1541	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.5095	838	1541	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	81.5079	890	1541	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.4788	842	1541	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	81.3662	924	1541	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.3133	865	1541	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.2861	929	1541	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.7728	762	1541	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.741	807	1541	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.7051	743	1541	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.6371	737	1541	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.5941	700	1541	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.3201	752	1541	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	80.1781	719	1541	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	79.9212	743	1541	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.9145	673	1541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,637] [INFO] DFAST Taxonomy check result was written to GCF_006346315.1_ASM634631v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference/checkm_data
[2024-01-24 13:41:22,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:22,686] [INFO] Task started: CheckM
[2024-01-24 13:41:22,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006346315.1_ASM634631v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006346315.1_ASM634631v1_genomic.fna/checkm_input GCF_006346315.1_ASM634631v1_genomic.fna/checkm_result
[2024-01-24 13:42:28,996] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:28,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,020] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:29,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:29,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006346315.1_ASM634631v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:29,021] [INFO] Task started: Blastn
[2024-01-24 13:42:29,021] [INFO] Running command: blastn -query GCF_006346315.1_ASM634631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54266272-03b5-4266-9099-433d0ccb20eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_006346315.1_ASM634631v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:31,293] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:31,296] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:31,297] [INFO] Target genome list was writen to GCF_006346315.1_ASM634631v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:31,358] [INFO] Task started: fastANI
[2024-01-24 13:42:31,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c47d50-80d8-4f63-863c-52d0a20efae3/GCF_006346315.1_ASM634631v1_genomic.fna.gz --refList GCF_006346315.1_ASM634631v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006346315.1_ASM634631v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:47,393] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:47,409] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:47,409] [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_006346315.1	s__Nocardioides litoris	100.0	1541	1541	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_008087085.1	s__Nocardioides rubriscoriae	84.1526	1063	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346395.1	s__Nocardioides plantarum	83.9235	1037	1541	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	83.3326	995	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_004522105.1	s__Nocardioides sp004522105	82.9894	1004	1541	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	81.7376	862	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_009823805.1	s__Nocardioides sp009823805	81.3164	865	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.2921	926	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002729525.1	s__Nocardioides sp002729525	81.2827	869	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698575.1	s__Nocardioides sp002698575	81.281	736	1541	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	80.9858	770	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_014191495.1	s__Nocardioides soli	80.7112	811	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:47,411] [INFO] GTDB search result was written to GCF_006346315.1_ASM634631v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:47,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:47,420] [INFO] DFAST_QC result json was written to GCF_006346315.1_ASM634631v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:47,420] [INFO] DFAST_QC completed!
[2024-01-24 13:42:47,420] [INFO] Total running time: 0h2m3s