[2024-01-24 13:41:20,485] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,489] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference
[2024-01-24 13:41:21,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,844] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg1042542f-0965-494b-94ce-1fe49d66ad0b/GCF_003350445.1_ASM335044v1_genomic.fna.gz | prodigal -d GCF_003350445.1_ASM335044v1_genomic.fna/cds.fna -a GCF_003350445.1_ASM335044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:51,856] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:51,856] [INFO] Task started: HMMsearch
[2024-01-24 13:41:51,856] [INFO] Running command: hmmsearch --tblout GCF_003350445.1_ASM335044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference/reference_markers.hmm GCF_003350445.1_ASM335044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:52,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:52,356] [INFO] Found 6/6 markers.
[2024-01-24 13:41:52,436] [INFO] Query marker FASTA was written to GCF_003350445.1_ASM335044v1_genomic.fna/markers.fasta
[2024-01-24 13:41:52,437] [INFO] Task started: Blastn
[2024-01-24 13:41:52,437] [INFO] Running command: blastn -query GCF_003350445.1_ASM335044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference/reference_markers.fasta -out GCF_003350445.1_ASM335044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,797] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:53,798] [INFO] Target genome list was writen to GCF_003350445.1_ASM335044v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:53,803] [INFO] Task started: fastANI
[2024-01-24 13:41:53,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg1042542f-0965-494b-94ce-1fe49d66ad0b/GCF_003350445.1_ASM335044v1_genomic.fna.gz --refList GCF_003350445.1_ASM335044v1_genomic.fna/target_genomes.txt --output GCF_003350445.1_ASM335044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:21,735] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:21,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:21,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:21,746] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:42:21,747] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:42:21,747] [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 flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	100.0	3140	3141	95	inconclusive
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	96.311	2594	3141	95	inconclusive
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	94.0127	2316	3141	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	93.9996	2272	3141	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	93.9977	2340	3141	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	91.2973	2377	3141	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	91.2785	2455	3141	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.0328	2259	3141	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	87.6525	2175	3141	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.3142	1647	3141	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0689	1155	3141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,750] [INFO] DFAST Taxonomy check result was written to GCF_003350445.1_ASM335044v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:21,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:21,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:21,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference/checkm_data
[2024-01-24 13:42:21,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:21,842] [INFO] Task started: CheckM
[2024-01-24 13:42:21,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350445.1_ASM335044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350445.1_ASM335044v1_genomic.fna/checkm_input GCF_003350445.1_ASM335044v1_genomic.fna/checkm_result
[2024-01-24 13:44:16,232] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:16,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:16,258] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:16,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:16,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350445.1_ASM335044v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:16,259] [INFO] Task started: Blastn
[2024-01-24 13:44:16,260] [INFO] Running command: blastn -query GCF_003350445.1_ASM335044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5cbef96-9c6f-4579-bdf2-35fa4ada8f01/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350445.1_ASM335044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:18,279] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:18,284] [INFO] Selected 13 target genomes.
[2024-01-24 13:44:18,284] [INFO] Target genome list was writen to GCF_003350445.1_ASM335044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:18,324] [INFO] Task started: fastANI
[2024-01-24 13:44:18,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg1042542f-0965-494b-94ce-1fe49d66ad0b/GCF_003350445.1_ASM335044v1_genomic.fna.gz --refList GCF_003350445.1_ASM335044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350445.1_ASM335044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:50,050] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:50,068] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:50,068] [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_003350445.1	s__Lentzea flaviverrucosa	100.0	3140	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000719115.1	s__Lentzea albidocapillata	94.0075	2316	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_900100275.1	s__Lentzea violacea	93.984	2274	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_900115955.1	s__Lentzea waywayandensis	91.2981	2452	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	91.2902	2378	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653695.1	s__Lentzea cavernae	90.5391	2396	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	88.2944	2284	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269295.1	s__Lentzea atacamensis	87.7764	2192	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_014648475.1	s__Lentzea flava	87.6492	2166	3141	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	87.4993	2100	3141	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	87.4153	2130	3141	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	86.589	2199	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845675.1	s__Lentzea sp007845675	82.3202	1645	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:50,070] [INFO] GTDB search result was written to GCF_003350445.1_ASM335044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:50,070] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:50,074] [INFO] DFAST_QC result json was written to GCF_003350445.1_ASM335044v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:50,074] [INFO] DFAST_QC completed!
[2024-01-24 13:44:50,074] [INFO] Total running time: 0h3m30s