[2024-01-24 12:53:36,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference
[2024-01-24 12:53:37,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,424] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgd83b8753-8470-4996-8bb5-c19a70cc9313/GCF_009805705.1_ASM980570v1_genomic.fna.gz | prodigal -d GCF_009805705.1_ASM980570v1_genomic.fna/cds.fna -a GCF_009805705.1_ASM980570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:50,975] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:50,976] [INFO] Task started: HMMsearch
[2024-01-24 12:53:50,976] [INFO] Running command: hmmsearch --tblout GCF_009805705.1_ASM980570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference/reference_markers.hmm GCF_009805705.1_ASM980570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:51,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:51,271] [INFO] Found 6/6 markers.
[2024-01-24 12:53:51,313] [INFO] Query marker FASTA was written to GCF_009805705.1_ASM980570v1_genomic.fna/markers.fasta
[2024-01-24 12:53:51,314] [INFO] Task started: Blastn
[2024-01-24 12:53:51,314] [INFO] Running command: blastn -query GCF_009805705.1_ASM980570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference/reference_markers.fasta -out GCF_009805705.1_ASM980570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:52,317] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:52,320] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:52,321] [INFO] Target genome list was writen to GCF_009805705.1_ASM980570v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:52,332] [INFO] Task started: fastANI
[2024-01-24 12:53:52,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgd83b8753-8470-4996-8bb5-c19a70cc9313/GCF_009805705.1_ASM980570v1_genomic.fna.gz --refList GCF_009805705.1_ASM980570v1_genomic.fna/target_genomes.txt --output GCF_009805705.1_ASM980570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:05,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:05,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:05,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:05,285] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:05,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:05,286] [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
Ruania rhizosphaerae	strain=LNNU 22110	GCA_009805705.1	1840413	1840413	type	True	100.0	1454	1455	95	conclusive
Ruania alkalisoli	strain=RN3S43	GCA_014960965.1	2779775	2779775	type	True	93.0818	1188	1455	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	83.2484	861	1455	95	below_threshold
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	82.5158	907	1455	95	below_threshold
Ruania halotolerans	strain=M4N3S171	GCA_021049285.1	2897773	2897773	type	True	81.5901	830	1455	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	79.1679	538	1455	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	79.0423	558	1455	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	78.6331	516	1455	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	78.5424	517	1455	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.7735	272	1455	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.6372	300	1455	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	77.2235	260	1455	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	77.0897	156	1455	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.6419	180	1455	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	75.8808	182	1455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:05,287] [INFO] DFAST Taxonomy check result was written to GCF_009805705.1_ASM980570v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:05,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:05,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:05,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference/checkm_data
[2024-01-24 12:54:05,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:05,330] [INFO] Task started: CheckM
[2024-01-24 12:54:05,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009805705.1_ASM980570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009805705.1_ASM980570v1_genomic.fna/checkm_input GCF_009805705.1_ASM980570v1_genomic.fna/checkm_result
[2024-01-24 12:54:52,473] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:52,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:52,498] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:52,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:52,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009805705.1_ASM980570v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:52,499] [INFO] Task started: Blastn
[2024-01-24 12:54:52,499] [INFO] Running command: blastn -query GCF_009805705.1_ASM980570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1252d93-6275-4ca5-bb16-c707d8b23976/dqc_reference/reference_markers_gtdb.fasta -out GCF_009805705.1_ASM980570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:53,938] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:53,942] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:53,942] [INFO] Target genome list was writen to GCF_009805705.1_ASM980570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:53,964] [INFO] Task started: fastANI
[2024-01-24 12:54:53,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgd83b8753-8470-4996-8bb5-c19a70cc9313/GCF_009805705.1_ASM980570v1_genomic.fna.gz --refList GCF_009805705.1_ASM980570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009805705.1_ASM980570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:05,214] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:05,236] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:05,237] [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_009805705.1	s__Haloactinobacterium sp009805705	100.0	1454	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014960965.1	s__Haloactinobacterium sp014960965	93.0973	1187	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105765.1	s__Haloactinobacterium album	82.5357	903	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421225.1	s__Ruania albidiflava	79.1767	537	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000995.1	s__Ruania sp008000995	79.0295	560	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	99.97	99.97	0.98	0.98	2	-
GCA_019116305.1	s__Ruania gallistercoris	79.0213	477	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353825.1	s__Occultella glacieicola	78.6855	503	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708215.1	s__Occultella sp009708215	78.6249	517	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	77.6415	299	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013149785.1	s__Isoptericola halotolerans	77.5882	281	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991205.1	s__Georgenia sp003991205	77.5123	270	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023105.1	s__Beutenbergia cavernae	77.1424	308	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Beutenbergia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	76.9753	273	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:05,239] [INFO] GTDB search result was written to GCF_009805705.1_ASM980570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:05,239] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:05,243] [INFO] DFAST_QC result json was written to GCF_009805705.1_ASM980570v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:05,243] [INFO] DFAST_QC completed!
[2024-01-24 12:55:05,243] [INFO] Total running time: 0h1m29s