[2024-01-24 12:44:43,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference
[2024-01-24 12:44:45,066] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,067] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,067] [INFO] Running command: gunzip -c /var/lib/cwl/stg472f1d9f-5a8e-40a7-8e06-246612a0ad1b/GCF_004364585.1_ASM436458v1_genomic.fna.gz | prodigal -d GCF_004364585.1_ASM436458v1_genomic.fna/cds.fna -a GCF_004364585.1_ASM436458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:53,718] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:53,718] [INFO] Task started: HMMsearch
[2024-01-24 12:44:53,718] [INFO] Running command: hmmsearch --tblout GCF_004364585.1_ASM436458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference/reference_markers.hmm GCF_004364585.1_ASM436458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,058] [INFO] Found 6/6 markers.
[2024-01-24 12:44:54,085] [INFO] Query marker FASTA was written to GCF_004364585.1_ASM436458v1_genomic.fna/markers.fasta
[2024-01-24 12:44:54,085] [INFO] Task started: Blastn
[2024-01-24 12:44:54,085] [INFO] Running command: blastn -query GCF_004364585.1_ASM436458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference/reference_markers.fasta -out GCF_004364585.1_ASM436458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,372] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,375] [INFO] Selected 10 target genomes.
[2024-01-24 12:44:55,376] [INFO] Target genome list was writen to GCF_004364585.1_ASM436458v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,379] [INFO] Task started: fastANI
[2024-01-24 12:44:55,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg472f1d9f-5a8e-40a7-8e06-246612a0ad1b/GCF_004364585.1_ASM436458v1_genomic.fna.gz --refList GCF_004364585.1_ASM436458v1_genomic.fna/target_genomes.txt --output GCF_004364585.1_ASM436458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:03,269] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:03,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:03,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:03,280] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:03,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:03,280] [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
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	100.0	971	972	95	conclusive
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	87.5714	797	972	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	87.3796	803	972	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	84.1504	692	972	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	84.0518	698	972	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.1882	303	972	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	79.1366	354	972	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	77.1404	167	972	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	76.8805	151	972	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.2109	155	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:03,282] [INFO] DFAST Taxonomy check result was written to GCF_004364585.1_ASM436458v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:03,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:03,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:03,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference/checkm_data
[2024-01-24 12:45:03,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:03,318] [INFO] Task started: CheckM
[2024-01-24 12:45:03,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364585.1_ASM436458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364585.1_ASM436458v1_genomic.fna/checkm_input GCF_004364585.1_ASM436458v1_genomic.fna/checkm_result
[2024-01-24 12:45:34,754] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:34,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:34,777] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:34,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:34,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364585.1_ASM436458v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:34,778] [INFO] Task started: Blastn
[2024-01-24 12:45:34,779] [INFO] Running command: blastn -query GCF_004364585.1_ASM436458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddf9d75f-e09f-44f2-9d20-fb8ad3d037de/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364585.1_ASM436458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:36,547] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:36,551] [INFO] Selected 7 target genomes.
[2024-01-24 12:45:36,552] [INFO] Target genome list was writen to GCF_004364585.1_ASM436458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:36,567] [INFO] Task started: fastANI
[2024-01-24 12:45:36,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg472f1d9f-5a8e-40a7-8e06-246612a0ad1b/GCF_004364585.1_ASM436458v1_genomic.fna.gz --refList GCF_004364585.1_ASM436458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364585.1_ASM436458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:41,750] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:41,758] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:41,758] [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_004364585.1	s__Nesterenkonia aurantiaca	100.0	971	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	conclusive
GCF_017347085.1	s__Nesterenkonia sp017347085	93.9768	858	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003003175.1	s__Nesterenkonia sandarakina_A	88.6165	825	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410215.1	s__Nesterenkonia sandarakina	87.3796	803	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_014873955.1	s__Nesterenkonia lutea	84.1089	695	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874065.1	s__Nesterenkonia halotolerans	84.0518	698	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019173455.1	s__Nesterenkonia sp019173455	83.4818	720	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:41,808] [INFO] GTDB search result was written to GCF_004364585.1_ASM436458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:41,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:41,814] [INFO] DFAST_QC result json was written to GCF_004364585.1_ASM436458v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:41,815] [INFO] DFAST_QC completed!
[2024-01-24 12:45:41,815] [INFO] Total running time: 0h0m58s