[2024-01-24 14:46:55,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference
[2024-01-24 14:46:58,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,023] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f952adb-67f8-40b3-8674-f6868e731b75/GCF_006352065.1_ASM635206v1_genomic.fna.gz | prodigal -d GCF_006352065.1_ASM635206v1_genomic.fna/cds.fna -a GCF_006352065.1_ASM635206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:10,827] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:10,828] [INFO] Task started: HMMsearch
[2024-01-24 14:47:10,828] [INFO] Running command: hmmsearch --tblout GCF_006352065.1_ASM635206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference/reference_markers.hmm GCF_006352065.1_ASM635206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:11,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:11,124] [INFO] Found 6/6 markers.
[2024-01-24 14:47:11,174] [INFO] Query marker FASTA was written to GCF_006352065.1_ASM635206v1_genomic.fna/markers.fasta
[2024-01-24 14:47:11,175] [INFO] Task started: Blastn
[2024-01-24 14:47:11,175] [INFO] Running command: blastn -query GCF_006352065.1_ASM635206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference/reference_markers.fasta -out GCF_006352065.1_ASM635206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:12,484] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:12,488] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:12,489] [INFO] Target genome list was writen to GCF_006352065.1_ASM635206v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:12,495] [INFO] Task started: fastANI
[2024-01-24 14:47:12,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f952adb-67f8-40b3-8674-f6868e731b75/GCF_006352065.1_ASM635206v1_genomic.fna.gz --refList GCF_006352065.1_ASM635206v1_genomic.fna/target_genomes.txt --output GCF_006352065.1_ASM635206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:26,252] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:26,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:26,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:26,268] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:26,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:26,268] [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
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	100.0	1389	1390	95	conclusive
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	83.5956	794	1390	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	83.3959	876	1390	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	83.1839	870	1390	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	81.3391	678	1390	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	81.1485	722	1390	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	80.9067	694	1390	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	79.4799	552	1390	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	79.3799	542	1390	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	77.9636	372	1390	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	77.761	474	1390	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.7218	458	1390	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.705	469	1390	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.6952	451	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:26,270] [INFO] DFAST Taxonomy check result was written to GCF_006352065.1_ASM635206v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:26,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:26,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:26,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference/checkm_data
[2024-01-24 14:47:26,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:26,315] [INFO] Task started: CheckM
[2024-01-24 14:47:26,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006352065.1_ASM635206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006352065.1_ASM635206v1_genomic.fna/checkm_input GCF_006352065.1_ASM635206v1_genomic.fna/checkm_result
[2024-01-24 14:48:21,138] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:21,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:21,163] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:21,164] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:21,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006352065.1_ASM635206v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:21,164] [INFO] Task started: Blastn
[2024-01-24 14:48:21,165] [INFO] Running command: blastn -query GCF_006352065.1_ASM635206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg720502f4-805f-452f-b625-22f4874d6328/dqc_reference/reference_markers_gtdb.fasta -out GCF_006352065.1_ASM635206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:23,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:23,095] [INFO] Selected 12 target genomes.
[2024-01-24 14:48:23,095] [INFO] Target genome list was writen to GCF_006352065.1_ASM635206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:23,103] [INFO] Task started: fastANI
[2024-01-24 14:48:23,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f952adb-67f8-40b3-8674-f6868e731b75/GCF_006352065.1_ASM635206v1_genomic.fna.gz --refList GCF_006352065.1_ASM635206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006352065.1_ASM635206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:34,912] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:34,927] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:34,927] [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_006352065.1	s__Georgenia sp006352065	100.0	1390	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	conclusive
GCF_009193185.1	s__Georgenia thermotolerans	83.4414	872	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009193175.1	s__Georgenia ruanii	83.2102	867	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991205.1	s__Georgenia sp003991205	82.0397	819	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193155.1	s__Georgenia subflava	81.2044	737	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002563695.1	s__Georgenia soli	81.1945	715	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814705.1	s__Georgenia muralis	80.8762	697	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014837105.1	s__Oceanitalea sp014837105	79.3432	546	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710105.1	s__Georgenia_A faecalis	79.3145	530	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia_A	95.0	99.15	99.15	0.96	0.96	2	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	79.2707	550	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902703175.1	s__Occultella aeris	77.7109	460	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353825.1	s__Occultella glacieicola	77.703	450	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:34,929] [INFO] GTDB search result was written to GCF_006352065.1_ASM635206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:34,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:34,934] [INFO] DFAST_QC result json was written to GCF_006352065.1_ASM635206v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:34,935] [INFO] DFAST_QC completed!
[2024-01-24 14:48:34,935] [INFO] Total running time: 0h1m39s