[2024-01-24 10:57:39,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:39,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:39,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference
[2024-01-24 10:57:40,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,336] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,336] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9506974-514f-4aed-9a83-593103407c8e/GCF_006349365.1_ASM634936v1_genomic.fna.gz | prodigal -d GCF_006349365.1_ASM634936v1_genomic.fna/cds.fna -a GCF_006349365.1_ASM634936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:49,645] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:49,645] [INFO] Task started: HMMsearch
[2024-01-24 10:57:49,645] [INFO] Running command: hmmsearch --tblout GCF_006349365.1_ASM634936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference/reference_markers.hmm GCF_006349365.1_ASM634936v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:49,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:49,914] [INFO] Found 6/6 markers.
[2024-01-24 10:57:49,948] [INFO] Query marker FASTA was written to GCF_006349365.1_ASM634936v1_genomic.fna/markers.fasta
[2024-01-24 10:57:49,948] [INFO] Task started: Blastn
[2024-01-24 10:57:49,948] [INFO] Running command: blastn -query GCF_006349365.1_ASM634936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference/reference_markers.fasta -out GCF_006349365.1_ASM634936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:51,259] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:51,267] [INFO] Selected 10 target genomes.
[2024-01-24 10:57:51,268] [INFO] Target genome list was writen to GCF_006349365.1_ASM634936v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:51,272] [INFO] Task started: fastANI
[2024-01-24 10:57:51,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9506974-514f-4aed-9a83-593103407c8e/GCF_006349365.1_ASM634936v1_genomic.fna.gz --refList GCF_006349365.1_ASM634936v1_genomic.fna/target_genomes.txt --output GCF_006349365.1_ASM634936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,090] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,101] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,101] [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 wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	100.0	1151	1151	95	conclusive
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	85.38	874	1151	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	81.3793	660	1151	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	79.8424	572	1151	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	79.6466	587	1151	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	79.6129	540	1151	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	79.4737	535	1151	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	79.3741	592	1151	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.0542	469	1151	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	77.6963	450	1151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,103] [INFO] DFAST Taxonomy check result was written to GCF_006349365.1_ASM634936v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference/checkm_data
[2024-01-24 10:58:01,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:01,140] [INFO] Task started: CheckM
[2024-01-24 10:58:01,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006349365.1_ASM634936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006349365.1_ASM634936v1_genomic.fna/checkm_input GCF_006349365.1_ASM634936v1_genomic.fna/checkm_result
[2024-01-24 10:58:54,818] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:54,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,842] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:54,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:54,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006349365.1_ASM634936v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:54,843] [INFO] Task started: Blastn
[2024-01-24 10:58:54,843] [INFO] Running command: blastn -query GCF_006349365.1_ASM634936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402b47c5-751a-45d8-a723-2303d4ac4dda/dqc_reference/reference_markers_gtdb.fasta -out GCF_006349365.1_ASM634936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:56,862] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:56,865] [INFO] Selected 6 target genomes.
[2024-01-24 10:58:56,865] [INFO] Target genome list was writen to GCF_006349365.1_ASM634936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:56,870] [INFO] Task started: fastANI
[2024-01-24 10:58:56,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9506974-514f-4aed-9a83-593103407c8e/GCF_006349365.1_ASM634936v1_genomic.fna.gz --refList GCF_006349365.1_ASM634936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006349365.1_ASM634936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:03,471] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:03,480] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:03,480] [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_006349365.1	s__Oceanitalea sp006349365	100.0	1151	1151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	99.20	99.20	0.95	0.95	2	conclusive
GCA_014837105.1	s__Oceanitalea sp014837105	85.3766	874	1151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193135.1	s__Oceanitalea satyanarayanai	85.1974	825	1151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	85.1299	851	1151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003710105.1	s__Georgenia_A faecalis	81.3977	658	1151	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_002563695.1	s__Georgenia soli	79.6147	582	1151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:03,482] [INFO] GTDB search result was written to GCF_006349365.1_ASM634936v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:03,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:03,486] [INFO] DFAST_QC result json was written to GCF_006349365.1_ASM634936v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:03,486] [INFO] DFAST_QC completed!
[2024-01-24 10:59:03,486] [INFO] Total running time: 0h1m24s