[2024-01-24 14:31:00,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,106] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,107] [INFO] Running command: gunzip -c /var/lib/cwl/stga46b3e5d-8de0-4428-9de0-985a9449922d/GCF_902703175.1_F300_genomic.fna.gz | prodigal -d GCF_902703175.1_F300_genomic.fna/cds.fna -a GCF_902703175.1_F300_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:17,414] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:17,415] [INFO] Task started: HMMsearch
[2024-01-24 14:31:17,415] [INFO] Running command: hmmsearch --tblout GCF_902703175.1_F300_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference/reference_markers.hmm GCF_902703175.1_F300_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:17,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:17,794] [INFO] Found 6/6 markers.
[2024-01-24 14:31:17,840] [INFO] Query marker FASTA was written to GCF_902703175.1_F300_genomic.fna/markers.fasta
[2024-01-24 14:31:17,841] [INFO] Task started: Blastn
[2024-01-24 14:31:17,841] [INFO] Running command: blastn -query GCF_902703175.1_F300_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference/reference_markers.fasta -out GCF_902703175.1_F300_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,937] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,939] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:18,940] [INFO] Target genome list was writen to GCF_902703175.1_F300_genomic.fna/target_genomes.txt
[2024-01-24 14:31:18,943] [INFO] Task started: fastANI
[2024-01-24 14:31:18,943] [INFO] Running command: fastANI --query /var/lib/cwl/stga46b3e5d-8de0-4428-9de0-985a9449922d/GCF_902703175.1_F300_genomic.fna.gz --refList GCF_902703175.1_F300_genomic.fna/target_genomes.txt --output GCF_902703175.1_F300_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:31,885] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:31,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:31,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:31,894] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:31,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:31,894] [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
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	100.0	1908	1916	95	conclusive
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	93.9612	1664	1916	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	91.7279	1555	1916	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	86.8997	1430	1916	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	79.0583	596	1916	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	78.8431	560	1916	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	78.7777	622	1916	95	below_threshold
Ruania alkalisoli	strain=RN3S43	GCA_014960965.1	2779775	2779775	type	True	78.141	525	1916	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.8934	444	1916	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	77.641	489	1916	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	77.5369	508	1916	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	77.433	398	1916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:31,896] [INFO] DFAST Taxonomy check result was written to GCF_902703175.1_F300_genomic.fna/tc_result.tsv
[2024-01-24 14:31:31,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:31,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:31,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference/checkm_data
[2024-01-24 14:31:31,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:31,951] [INFO] Task started: CheckM
[2024-01-24 14:31:31,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902703175.1_F300_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902703175.1_F300_genomic.fna/checkm_input GCF_902703175.1_F300_genomic.fna/checkm_result
[2024-01-24 14:32:36,846] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:36,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:36,861] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:36,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:36,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902703175.1_F300_genomic.fna/markers.fasta)
[2024-01-24 14:32:36,862] [INFO] Task started: Blastn
[2024-01-24 14:32:36,862] [INFO] Running command: blastn -query GCF_902703175.1_F300_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a70791b-7c36-46af-b036-f0db3ebd23d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_902703175.1_F300_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:38,536] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:38,538] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:38,538] [INFO] Target genome list was writen to GCF_902703175.1_F300_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:38,546] [INFO] Task started: fastANI
[2024-01-24 14:32:38,546] [INFO] Running command: fastANI --query /var/lib/cwl/stga46b3e5d-8de0-4428-9de0-985a9449922d/GCF_902703175.1_F300_genomic.fna.gz --refList GCF_902703175.1_F300_genomic.fna/target_genomes_gtdb.txt --output GCF_902703175.1_F300_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:52,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:52,734] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:52,734] [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_902703175.1	s__Occultella aeris	100.0	1908	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009708215.1	s__Occultella sp009708215	93.9612	1664	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_004353825.1	s__Occultella glacieicola	86.9066	1429	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649925.1	s__JAENWO01 sp016649925	79.6224	417	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__JAENWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421225.1	s__Ruania albidiflava	79.077	593	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105765.1	s__Haloactinobacterium album	78.8443	594	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000995.1	s__Ruania sp008000995	78.8003	619	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009733795.1	s__Pseudactinotalea caeni	78.6088	610	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014960965.1	s__Haloactinobacterium sp014960965	78.152	524	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009660225.1	s__HY158 sp009660225	77.9604	401	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__HY158	95.0	98.70	98.70	0.90	0.90	2	-
GCF_006352065.1	s__Georgenia sp006352065	77.8909	444	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_009193175.1	s__Georgenia ruanii	77.6462	489	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003755175.1	s__Cellulomonas sp003755175	77.6122	418	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	77.3309	452	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCA_018316655.1	s__Nocardiopsis sp018316655	75.8633	358	1916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:52,736] [INFO] GTDB search result was written to GCF_902703175.1_F300_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:52,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:52,739] [INFO] DFAST_QC result json was written to GCF_902703175.1_F300_genomic.fna/dqc_result.json
[2024-01-24 14:32:52,740] [INFO] DFAST_QC completed!
[2024-01-24 14:32:52,740] [INFO] Total running time: 0h1m52s