[2024-01-24 13:45:58,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:58,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:58,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference
[2024-01-24 13:45:59,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:59,997] [INFO] Task started: Prodigal
[2024-01-24 13:45:59,997] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0996757-c140-48d6-a1ce-32b7e92f17be/GCF_014960965.1_ASM1496096v1_genomic.fna.gz | prodigal -d GCF_014960965.1_ASM1496096v1_genomic.fna/cds.fna -a GCF_014960965.1_ASM1496096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:13,972] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:13,972] [INFO] Task started: HMMsearch
[2024-01-24 13:46:13,972] [INFO] Running command: hmmsearch --tblout GCF_014960965.1_ASM1496096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference/reference_markers.hmm GCF_014960965.1_ASM1496096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:14,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:14,293] [INFO] Found 6/6 markers.
[2024-01-24 13:46:14,336] [INFO] Query marker FASTA was written to GCF_014960965.1_ASM1496096v1_genomic.fna/markers.fasta
[2024-01-24 13:46:14,336] [INFO] Task started: Blastn
[2024-01-24 13:46:14,336] [INFO] Running command: blastn -query GCF_014960965.1_ASM1496096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference/reference_markers.fasta -out GCF_014960965.1_ASM1496096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:15,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:15,496] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:15,497] [INFO] Target genome list was writen to GCF_014960965.1_ASM1496096v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:15,516] [INFO] Task started: fastANI
[2024-01-24 13:46:15,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0996757-c140-48d6-a1ce-32b7e92f17be/GCF_014960965.1_ASM1496096v1_genomic.fna.gz --refList GCF_014960965.1_ASM1496096v1_genomic.fna/target_genomes.txt --output GCF_014960965.1_ASM1496096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:27,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:27,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:27,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:27,451] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:27,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:27,451] [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 alkalisoli	strain=RN3S43	GCA_014960965.1	2779775	2779775	type	True	100.0	1482	1482	95	conclusive
Ruania rhizosphaerae	strain=LNNU 22110	GCA_009805705.1	1840413	1840413	type	True	93.0563	1197	1482	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	83.1125	878	1482	95	below_threshold
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	82.8041	932	1482	95	below_threshold
Ruania halotolerans	strain=M4N3S171	GCA_021049285.1	2897773	2897773	type	True	81.8707	832	1482	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	79.1393	531	1482	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	79.0395	538	1482	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	78.5505	511	1482	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	78.1774	516	1482	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	77.134	268	1482	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	76.5881	190	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:27,453] [INFO] DFAST Taxonomy check result was written to GCF_014960965.1_ASM1496096v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:27,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:27,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:27,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference/checkm_data
[2024-01-24 13:46:27,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:27,501] [INFO] Task started: CheckM
[2024-01-24 13:46:27,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014960965.1_ASM1496096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014960965.1_ASM1496096v1_genomic.fna/checkm_input GCF_014960965.1_ASM1496096v1_genomic.fna/checkm_result
[2024-01-24 13:47:23,329] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:23,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,353] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:23,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:23,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014960965.1_ASM1496096v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:23,354] [INFO] Task started: Blastn
[2024-01-24 13:47:23,355] [INFO] Running command: blastn -query GCF_014960965.1_ASM1496096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f952f3b-f095-4e2c-a7cf-6a561e63e187/dqc_reference/reference_markers_gtdb.fasta -out GCF_014960965.1_ASM1496096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:24,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:24,888] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:24,889] [INFO] Target genome list was writen to GCF_014960965.1_ASM1496096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:24,901] [INFO] Task started: fastANI
[2024-01-24 13:47:24,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0996757-c140-48d6-a1ce-32b7e92f17be/GCF_014960965.1_ASM1496096v1_genomic.fna.gz --refList GCF_014960965.1_ASM1496096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014960965.1_ASM1496096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:34,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:34,877] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:34,878] [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_014960965.1	s__Haloactinobacterium sp014960965	100.0	1482	1482	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_009805705.1	s__Haloactinobacterium sp009805705	93.0563	1197	1482	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	82.7809	937	1482	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	79.1216	533	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000421225.1	s__Ruania albidiflava	79.0651	537	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116305.1	s__Ruania gallistercoris	78.8095	491	1482	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	78.6964	496	1482	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	78.5136	511	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_902703175.1	s__Occultella aeris	78.1937	513	1482	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	77.8134	270	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__JAENWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149785.1	s__Isoptericola halotolerans	77.6326	268	1482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:34,879] [INFO] GTDB search result was written to GCF_014960965.1_ASM1496096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:34,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:34,883] [INFO] DFAST_QC result json was written to GCF_014960965.1_ASM1496096v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:34,883] [INFO] DFAST_QC completed!
[2024-01-24 13:47:34,883] [INFO] Total running time: 0h1m36s