[2024-01-25 18:17:05,465] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:17:05,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:17:05,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference
[2024-01-25 18:17:06,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:17:06,667] [INFO] Task started: Prodigal
[2024-01-25 18:17:06,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6f5ff12-f4ef-47d1-a0b8-a44a2a682705/GCF_003269295.1_ASM326929v1_genomic.fna.gz | prodigal -d GCF_003269295.1_ASM326929v1_genomic.fna/cds.fna -a GCF_003269295.1_ASM326929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:34,097] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:34,097] [INFO] Task started: HMMsearch
[2024-01-25 18:17:34,097] [INFO] Running command: hmmsearch --tblout GCF_003269295.1_ASM326929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference/reference_markers.hmm GCF_003269295.1_ASM326929v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:34,494] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:34,495] [INFO] Found 6/6 markers.
[2024-01-25 18:17:34,570] [INFO] Query marker FASTA was written to GCF_003269295.1_ASM326929v1_genomic.fna/markers.fasta
[2024-01-25 18:17:34,570] [INFO] Task started: Blastn
[2024-01-25 18:17:34,570] [INFO] Running command: blastn -query GCF_003269295.1_ASM326929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference/reference_markers.fasta -out GCF_003269295.1_ASM326929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:35,939] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:35,942] [INFO] Selected 17 target genomes.
[2024-01-25 18:17:35,942] [INFO] Target genome list was writen to GCF_003269295.1_ASM326929v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:35,981] [INFO] Task started: fastANI
[2024-01-25 18:17:35,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f5ff12-f4ef-47d1-a0b8-a44a2a682705/GCF_003269295.1_ASM326929v1_genomic.fna.gz --refList GCF_003269295.1_ASM326929v1_genomic.fna/target_genomes.txt --output GCF_003269295.1_ASM326929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:18:10,679] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:10,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:18:10,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:18:10,691] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:18:10,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:18:10,692] [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
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	100.0	3083	3086	95	conclusive
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	90.8561	2315	3086	95	below_threshold
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	90.8358	2317	3086	95	below_threshold
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	90.3769	2231	3086	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	89.6913	2424	3086	95	below_threshold
Lentzea indica	strain=PSKA42	GCA_012184385.1	2604800	2604800	type	True	89.5171	2153	3086	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.7925	2291	3086	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	87.7346	2185	3086	95	below_threshold
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	87.484	2008	3086	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	86.6178	2138	3086	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.6035	1646	3086	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	80.0056	1115	3086	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	79.7908	985	3086	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	78.1778	710	3086	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	78.1082	705	3086	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.0727	821	3086	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0347	1053	3086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:18:10,693] [INFO] DFAST Taxonomy check result was written to GCF_003269295.1_ASM326929v1_genomic.fna/tc_result.tsv
[2024-01-25 18:18:10,694] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:18:10,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:18:10,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference/checkm_data
[2024-01-25 18:18:10,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:18:10,776] [INFO] Task started: CheckM
[2024-01-25 18:18:10,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003269295.1_ASM326929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003269295.1_ASM326929v1_genomic.fna/checkm_input GCF_003269295.1_ASM326929v1_genomic.fna/checkm_result
[2024-01-25 18:20:33,749] [INFO] Task succeeded: CheckM
[2024-01-25 18:20:33,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:20:33,780] [INFO] ===== Completeness check finished =====
[2024-01-25 18:20:33,781] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:20:33,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003269295.1_ASM326929v1_genomic.fna/markers.fasta)
[2024-01-25 18:20:33,782] [INFO] Task started: Blastn
[2024-01-25 18:20:33,782] [INFO] Running command: blastn -query GCF_003269295.1_ASM326929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01eee601-8e4d-4af8-a8d6-1aa6a4476e97/dqc_reference/reference_markers_gtdb.fasta -out GCF_003269295.1_ASM326929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:35,865] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:35,868] [INFO] Selected 16 target genomes.
[2024-01-25 18:20:35,868] [INFO] Target genome list was writen to GCF_003269295.1_ASM326929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:20:35,891] [INFO] Task started: fastANI
[2024-01-25 18:20:35,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f5ff12-f4ef-47d1-a0b8-a44a2a682705/GCF_003269295.1_ASM326929v1_genomic.fna.gz --refList GCF_003269295.1_ASM326929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003269295.1_ASM326929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:10,548] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:10,558] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:21:10,559] [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_003269295.1	s__Lentzea atacamensis	100.0	3083	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	conclusive
GCF_014648475.1	s__Lentzea flava	90.8126	2321	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907955.1	s__Lentzea nigeriaca	90.377	2232	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265345.1	s__Lentzea terrae	89.6851	2424	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184385.1	s__Lentzea indica	89.5303	2150	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	88.9379	2185	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974445.1	s__Lentzea aerocolonigenes	88.8293	2301	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900110955.1	s__Lentzea xinjiangensis	87.8506	2036	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104175.1	s__Lentzea jiangxiensis	87.4783	2009	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111005.1	s__Lentzea albida	87.322	2151	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279525.1	s__Lentzea sp001279525	86.7583	2048	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001701025.1	s__Lentzea guizhouensis	86.6	2141	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	80.0211	1112	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	80.0065	1108	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	79.8142	979	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	78.1947	706	3086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:21:10,566] [INFO] GTDB search result was written to GCF_003269295.1_ASM326929v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:10,567] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:10,571] [INFO] DFAST_QC result json was written to GCF_003269295.1_ASM326929v1_genomic.fna/dqc_result.json
[2024-01-25 18:21:10,571] [INFO] DFAST_QC completed!
[2024-01-25 18:21:10,571] [INFO] Total running time: 0h4m5s