[2024-01-24 11:34:52,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:52,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:52,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference
[2024-01-24 11:34:55,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,643] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgb26adc33-91c3-4b96-b7b0-983280c01cc9/GCF_024648825.1_ASM2464882v1_genomic.fna.gz | prodigal -d GCF_024648825.1_ASM2464882v1_genomic.fna/cds.fna -a GCF_024648825.1_ASM2464882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:32,627] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:32,628] [INFO] Task started: HMMsearch
[2024-01-24 11:35:32,628] [INFO] Running command: hmmsearch --tblout GCF_024648825.1_ASM2464882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference/reference_markers.hmm GCF_024648825.1_ASM2464882v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:33,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:33,038] [INFO] Found 6/6 markers.
[2024-01-24 11:35:33,119] [INFO] Query marker FASTA was written to GCF_024648825.1_ASM2464882v1_genomic.fna/markers.fasta
[2024-01-24 11:35:33,119] [INFO] Task started: Blastn
[2024-01-24 11:35:33,119] [INFO] Running command: blastn -query GCF_024648825.1_ASM2464882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference/reference_markers.fasta -out GCF_024648825.1_ASM2464882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:34,540] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:34,544] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:34,545] [INFO] Target genome list was writen to GCF_024648825.1_ASM2464882v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:34,550] [INFO] Task started: fastANI
[2024-01-24 11:35:34,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26adc33-91c3-4b96-b7b0-983280c01cc9/GCF_024648825.1_ASM2464882v1_genomic.fna.gz --refList GCF_024648825.1_ASM2464882v1_genomic.fna/target_genomes.txt --output GCF_024648825.1_ASM2464882v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:59,658] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:59,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:59,672] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:59,672] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:59,672] [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 californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	100.0	2983	2986	95	inconclusive
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	96.29	2601	2986	95	inconclusive
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	94.1018	2262	2986	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	94.0462	2266	2986	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	93.9643	2220	2986	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	91.3523	2356	2986	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	91.2798	2379	2986	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.0548	2212	2986	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.2598	1620	2986	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	77.8559	807	2986	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.5314	629	2986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,674] [INFO] DFAST Taxonomy check result was written to GCF_024648825.1_ASM2464882v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:59,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:59,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:59,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference/checkm_data
[2024-01-24 11:35:59,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:59,767] [INFO] Task started: CheckM
[2024-01-24 11:35:59,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024648825.1_ASM2464882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024648825.1_ASM2464882v1_genomic.fna/checkm_input GCF_024648825.1_ASM2464882v1_genomic.fna/checkm_result
[2024-01-24 11:38:14,716] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:14,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:38:14,745] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:14,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:14,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024648825.1_ASM2464882v1_genomic.fna/markers.fasta)
[2024-01-24 11:38:14,746] [INFO] Task started: Blastn
[2024-01-24 11:38:14,747] [INFO] Running command: blastn -query GCF_024648825.1_ASM2464882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeecaa8f2-140a-4dc0-9c50-1867103c6943/dqc_reference/reference_markers_gtdb.fasta -out GCF_024648825.1_ASM2464882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:16,747] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:16,752] [INFO] Selected 11 target genomes.
[2024-01-24 11:38:16,752] [INFO] Target genome list was writen to GCF_024648825.1_ASM2464882v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:16,762] [INFO] Task started: fastANI
[2024-01-24 11:38:16,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26adc33-91c3-4b96-b7b0-983280c01cc9/GCF_024648825.1_ASM2464882v1_genomic.fna.gz --refList GCF_024648825.1_ASM2464882v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024648825.1_ASM2464882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:43,192] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:43,205] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:43,205] [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	96.2974	2600	2986	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	94.102	2262	2986	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	93.9741	2219	2986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	91.3381	2358	2986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115955.1	s__Lentzea waywayandensis	91.2618	2383	2986	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	90.5297	2387	2986	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	89.9017	2339	2986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648475.1	s__Lentzea flava	87.7077	2140	2986	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	87.5555	2042	2986	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	87.3524	2106	2986	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	82.3026	1610	2986	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 11:38:43,207] [INFO] GTDB search result was written to GCF_024648825.1_ASM2464882v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:43,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:43,211] [INFO] DFAST_QC result json was written to GCF_024648825.1_ASM2464882v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:43,211] [INFO] DFAST_QC completed!
[2024-01-24 11:38:43,212] [INFO] Total running time: 0h3m50s