[2024-01-24 14:23:20,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference
[2024-01-24 14:23:21,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:21,769] [INFO] Task started: Prodigal
[2024-01-24 14:23:21,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a93af12-0e27-43b6-9928-80f61bcbaf5c/GCF_009362315.1_ASM936231v1_genomic.fna.gz | prodigal -d GCF_009362315.1_ASM936231v1_genomic.fna/cds.fna -a GCF_009362315.1_ASM936231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:33,815] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:33,816] [INFO] Task started: HMMsearch
[2024-01-24 14:23:33,816] [INFO] Running command: hmmsearch --tblout GCF_009362315.1_ASM936231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference/reference_markers.hmm GCF_009362315.1_ASM936231v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:34,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:34,143] [INFO] Found 6/6 markers.
[2024-01-24 14:23:34,190] [INFO] Query marker FASTA was written to GCF_009362315.1_ASM936231v1_genomic.fna/markers.fasta
[2024-01-24 14:23:34,190] [INFO] Task started: Blastn
[2024-01-24 14:23:34,190] [INFO] Running command: blastn -query GCF_009362315.1_ASM936231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference/reference_markers.fasta -out GCF_009362315.1_ASM936231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:35,623] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:35,626] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:35,627] [INFO] Target genome list was writen to GCF_009362315.1_ASM936231v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:35,632] [INFO] Task started: fastANI
[2024-01-24 14:23:35,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a93af12-0e27-43b6-9928-80f61bcbaf5c/GCF_009362315.1_ASM936231v1_genomic.fna.gz --refList GCF_009362315.1_ASM936231v1_genomic.fna/target_genomes.txt --output GCF_009362315.1_ASM936231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:50,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:50,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:50,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:50,583] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:50,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:50,584] [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 subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	100.0	1321	1332	95	conclusive
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	99.9992	1330	1332	95	conclusive
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	82.158	749	1332	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	81.4644	700	1332	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	81.3893	665	1332	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	81.2537	681	1332	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	81.1734	666	1332	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	81.1473	692	1332	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	79.4984	519	1332	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	79.4544	513	1332	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	79.3905	561	1332	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.9291	461	1332	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.5802	432	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:50,585] [INFO] DFAST Taxonomy check result was written to GCF_009362315.1_ASM936231v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:50,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:50,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:50,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference/checkm_data
[2024-01-24 14:23:50,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:50,633] [INFO] Task started: CheckM
[2024-01-24 14:23:50,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009362315.1_ASM936231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009362315.1_ASM936231v1_genomic.fna/checkm_input GCF_009362315.1_ASM936231v1_genomic.fna/checkm_result
[2024-01-24 14:24:45,416] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:45,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:45,438] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:45,439] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:45,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009362315.1_ASM936231v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:45,440] [INFO] Task started: Blastn
[2024-01-24 14:24:45,440] [INFO] Running command: blastn -query GCF_009362315.1_ASM936231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c7b38d3-8b04-4d3c-83f8-77ac7a85adaa/dqc_reference/reference_markers_gtdb.fasta -out GCF_009362315.1_ASM936231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:47,490] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:47,494] [INFO] Selected 9 target genomes.
[2024-01-24 14:24:47,494] [INFO] Target genome list was writen to GCF_009362315.1_ASM936231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:47,508] [INFO] Task started: fastANI
[2024-01-24 14:24:47,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a93af12-0e27-43b6-9928-80f61bcbaf5c/GCF_009362315.1_ASM936231v1_genomic.fna.gz --refList GCF_009362315.1_ASM936231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009362315.1_ASM936231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:56,605] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:56,621] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:56,621] [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_009193155.1	s__Georgenia subflava	99.9992	1330	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002563695.1	s__Georgenia soli	82.1754	747	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193185.1	s__Georgenia thermotolerans	81.4287	703	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006352065.1	s__Georgenia sp006352065	81.2534	681	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_003814705.1	s__Georgenia muralis	81.1972	662	1332	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	81.1921	674	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193175.1	s__Georgenia ruanii	81.1091	696	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710105.1	s__Georgenia_A faecalis	79.4252	516	1332	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_003752405.1	s__Bogoriella caseilytica	78.3336	317	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Bogoriella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:56,623] [INFO] GTDB search result was written to GCF_009362315.1_ASM936231v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:56,623] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:56,627] [INFO] DFAST_QC result json was written to GCF_009362315.1_ASM936231v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:56,628] [INFO] DFAST_QC completed!
[2024-01-24 14:24:56,628] [INFO] Total running time: 0h1m36s