[2024-01-24 13:49:13,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:13,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:13,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference
[2024-01-24 13:49:15,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:15,086] [INFO] Task started: Prodigal
[2024-01-24 13:49:15,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg51c895aa-eaca-4cd0-8713-0f273c16b20f/GCF_014205135.1_ASM1420513v1_genomic.fna.gz | prodigal -d GCF_014205135.1_ASM1420513v1_genomic.fna/cds.fna -a GCF_014205135.1_ASM1420513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:41,247] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:41,248] [INFO] Task started: HMMsearch
[2024-01-24 13:49:41,248] [INFO] Running command: hmmsearch --tblout GCF_014205135.1_ASM1420513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference/reference_markers.hmm GCF_014205135.1_ASM1420513v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:41,636] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:41,638] [INFO] Found 6/6 markers.
[2024-01-24 13:49:41,711] [INFO] Query marker FASTA was written to GCF_014205135.1_ASM1420513v1_genomic.fna/markers.fasta
[2024-01-24 13:49:41,711] [INFO] Task started: Blastn
[2024-01-24 13:49:41,711] [INFO] Running command: blastn -query GCF_014205135.1_ASM1420513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference/reference_markers.fasta -out GCF_014205135.1_ASM1420513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,005] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,009] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:43,009] [INFO] Target genome list was writen to GCF_014205135.1_ASM1420513v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,020] [INFO] Task started: fastANI
[2024-01-24 13:49:43,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c895aa-eaca-4cd0-8713-0f273c16b20f/GCF_014205135.1_ASM1420513v1_genomic.fna.gz --refList GCF_014205135.1_ASM1420513v1_genomic.fna/target_genomes.txt --output GCF_014205135.1_ASM1420513v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:13,208] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:13,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:13,226] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:13,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:13,226] [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
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	100.0	2961	2961	95	conclusive
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	85.9712	1888	2961	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	84.1539	1854	2961	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	83.61	1530	2961	95	below_threshold
Kribbella catacumbae	strain=DSM 19601	GCA_000372465.1	460086	460086	type	True	83.4749	1759	2961	95	below_threshold
Kribbella monticola	strain=NEAU-SW521	GCA_003261635.1	2185285	2185285	type	True	83.277	1677	2961	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	83.067	1705	2961	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	82.8372	1640	2961	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	82.7922	1740	2961	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	82.7793	1668	2961	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	82.6788	1601	2961	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	82.614	1696	2961	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	82.2905	1499	2961	95	below_threshold
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	82.2096	1552	2961	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.9545	608	2961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,228] [INFO] DFAST Taxonomy check result was written to GCF_014205135.1_ASM1420513v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:13,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:13,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:13,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference/checkm_data
[2024-01-24 13:50:13,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:13,316] [INFO] Task started: CheckM
[2024-01-24 13:50:13,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205135.1_ASM1420513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205135.1_ASM1420513v1_genomic.fna/checkm_input GCF_014205135.1_ASM1420513v1_genomic.fna/checkm_result
[2024-01-24 13:51:41,016] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:41,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:41,038] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:41,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:41,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205135.1_ASM1420513v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:41,039] [INFO] Task started: Blastn
[2024-01-24 13:51:41,039] [INFO] Running command: blastn -query GCF_014205135.1_ASM1420513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg829d1193-7431-4e28-916d-03026f02bbc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205135.1_ASM1420513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:42,886] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:42,890] [INFO] Selected 13 target genomes.
[2024-01-24 13:51:42,890] [INFO] Target genome list was writen to GCF_014205135.1_ASM1420513v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:42,922] [INFO] Task started: fastANI
[2024-01-24 13:51:42,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c895aa-eaca-4cd0-8713-0f273c16b20f/GCF_014205135.1_ASM1420513v1_genomic.fna.gz --refList GCF_014205135.1_ASM1420513v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205135.1_ASM1420513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:10,376] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:10,387] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:10,387] [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_014205135.1	s__Kribbella italica	100.0	2961	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001984195.1	s__Kribbella sp001984195	88.2699	2103	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024345.1	s__Kribbella flavida	85.9739	1887	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828865.1	s__Kribbella amoyensis	84.1195	1859	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361855.1	s__Kribbella sp004361855	83.7052	1719	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345365.1	s__Kribbella sp004345365	83.444	1780	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.33	95.31	0.84	0.84	3	-
GCF_003261635.1	s__Kribbella monticola	83.2983	1673	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365175.1	s__Kribbella sp004365175	83.295	1719	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342025.1	s__Kribbella sp004342025	83.1429	1747	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761605.1	s__Kribbella shirazensis	82.845	1639	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	82.6737	1603	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233875.1	s__Kribbella sp005233875	82.6358	1692	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348455.1	s__Kribbella albertanoniae	82.5725	1577	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:10,389] [INFO] GTDB search result was written to GCF_014205135.1_ASM1420513v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:10,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:10,393] [INFO] DFAST_QC result json was written to GCF_014205135.1_ASM1420513v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:10,393] [INFO] DFAST_QC completed!
[2024-01-24 13:52:10,393] [INFO] Total running time: 0h2m57s