[2024-01-25 20:20:05,701] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference
[2024-01-25 20:20:06,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:06,838] [INFO] Task started: Prodigal
[2024-01-25 20:20:06,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ff3bd09-f13e-4504-bf45-40d8f1d4c382/GCF_011839805.1_ASM1183980v1_genomic.fna.gz | prodigal -d GCF_011839805.1_ASM1183980v1_genomic.fna/cds.fna -a GCF_011839805.1_ASM1183980v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:17,635] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:17,635] [INFO] Task started: HMMsearch
[2024-01-25 20:20:17,635] [INFO] Running command: hmmsearch --tblout GCF_011839805.1_ASM1183980v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference/reference_markers.hmm GCF_011839805.1_ASM1183980v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:17,866] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:17,867] [INFO] Found 6/6 markers.
[2024-01-25 20:20:17,906] [INFO] Query marker FASTA was written to GCF_011839805.1_ASM1183980v1_genomic.fna/markers.fasta
[2024-01-25 20:20:17,906] [INFO] Task started: Blastn
[2024-01-25 20:20:17,907] [INFO] Running command: blastn -query GCF_011839805.1_ASM1183980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference/reference_markers.fasta -out GCF_011839805.1_ASM1183980v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:19,177] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:19,180] [INFO] Selected 13 target genomes.
[2024-01-25 20:20:19,181] [INFO] Target genome list was writen to GCF_011839805.1_ASM1183980v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:19,210] [INFO] Task started: fastANI
[2024-01-25 20:20:19,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ff3bd09-f13e-4504-bf45-40d8f1d4c382/GCF_011839805.1_ASM1183980v1_genomic.fna.gz --refList GCF_011839805.1_ASM1183980v1_genomic.fna/target_genomes.txt --output GCF_011839805.1_ASM1183980v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:34,679] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:34,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:34,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:34,688] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:34,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:34,688] [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
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	100.0	1564	1567	95	conclusive
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	87.2809	965	1567	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	82.1048	788	1567	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	81.9007	909	1567	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	81.6073	676	1567	95	below_threshold
Kineococcus aurantiacus	strain=DSM 7487	GCA_013409345.1	37633	37633	type	True	81.4729	918	1567	95	below_threshold
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	81.2453	929	1567	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	79.6363	729	1567	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.011	437	1567	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.7252	489	1567	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.5004	384	1567	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.4362	385	1567	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.9949	599	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:34,689] [INFO] DFAST Taxonomy check result was written to GCF_011839805.1_ASM1183980v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:34,690] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:34,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:34,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference/checkm_data
[2024-01-25 20:20:34,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:34,737] [INFO] Task started: CheckM
[2024-01-25 20:20:34,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011839805.1_ASM1183980v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011839805.1_ASM1183980v1_genomic.fna/checkm_input GCF_011839805.1_ASM1183980v1_genomic.fna/checkm_result
[2024-01-25 20:21:30,056] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:30,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:30,080] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:30,080] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:30,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011839805.1_ASM1183980v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:30,081] [INFO] Task started: Blastn
[2024-01-25 20:21:30,081] [INFO] Running command: blastn -query GCF_011839805.1_ASM1183980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc71c174f-2c24-463b-9a16-740b038d7795/dqc_reference/reference_markers_gtdb.fasta -out GCF_011839805.1_ASM1183980v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:32,148] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:32,151] [INFO] Selected 7 target genomes.
[2024-01-25 20:21:32,151] [INFO] Target genome list was writen to GCF_011839805.1_ASM1183980v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:32,156] [INFO] Task started: fastANI
[2024-01-25 20:21:32,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ff3bd09-f13e-4504-bf45-40d8f1d4c382/GCF_011839805.1_ASM1183980v1_genomic.fna.gz --refList GCF_011839805.1_ASM1183980v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011839805.1_ASM1183980v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:41,450] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:41,456] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:41,456] [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_011839805.1	s__Kineococcus rubinsiae	100.0	1564	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009906795.1	s__Kineococcus siccus	87.2772	966	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906315.1	s__Kineococcus vitellinus	82.2069	776	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017305.1	s__Kineococcus radiotolerans	81.927	907	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	98.46	98.46	0.90	0.90	2	-
GCF_013409345.1	s__Kineococcus aurantiacus	81.4533	920	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002055.1	s__Kineococcus rhizosphaerae	81.2221	932	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934625.1	s__Kineococcus xinjiangensis	79.6274	730	1567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:41,457] [INFO] GTDB search result was written to GCF_011839805.1_ASM1183980v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:41,458] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:41,460] [INFO] DFAST_QC result json was written to GCF_011839805.1_ASM1183980v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:41,461] [INFO] DFAST_QC completed!
[2024-01-25 20:21:41,461] [INFO] Total running time: 0h1m36s