[2024-01-24 12:54:05,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference
[2024-01-24 12:54:07,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,725] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,725] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5ee4428-bffc-494e-b4a7-b7a8f07899de/GCF_024171805.1_ASM2417180v1_genomic.fna.gz | prodigal -d GCF_024171805.1_ASM2417180v1_genomic.fna/cds.fna -a GCF_024171805.1_ASM2417180v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:42,941] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:42,942] [INFO] Task started: HMMsearch
[2024-01-24 12:54:42,942] [INFO] Running command: hmmsearch --tblout GCF_024171805.1_ASM2417180v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference/reference_markers.hmm GCF_024171805.1_ASM2417180v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:43,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:43,527] [INFO] Found 6/6 markers.
[2024-01-24 12:54:43,620] [INFO] Query marker FASTA was written to GCF_024171805.1_ASM2417180v1_genomic.fna/markers.fasta
[2024-01-24 12:54:43,621] [INFO] Task started: Blastn
[2024-01-24 12:54:43,621] [INFO] Running command: blastn -query GCF_024171805.1_ASM2417180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference/reference_markers.fasta -out GCF_024171805.1_ASM2417180v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:45,221] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:45,226] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:45,226] [INFO] Target genome list was writen to GCF_024171805.1_ASM2417180v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:45,243] [INFO] Task started: fastANI
[2024-01-24 12:54:45,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ee4428-bffc-494e-b4a7-b7a8f07899de/GCF_024171805.1_ASM2417180v1_genomic.fna.gz --refList GCF_024171805.1_ASM2417180v1_genomic.fna/target_genomes.txt --output GCF_024171805.1_ASM2417180v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:24,294] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:24,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:24,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:24,309] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:55:24,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:24,310] [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 aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	99.9999	3519	3549	95	conclusive
Lentzea aerocolonigenes	strain=NBRC 13195	GCA_000974445.1	68170	68170	type	True	99.9938	3490	3549	95	conclusive
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	99.9757	3452	3549	95	conclusive
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	89.1381	2447	3549	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	89.1203	2382	3549	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	88.9849	2389	3549	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	88.7774	2523	3549	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	88.7444	2311	3549	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	88.0251	2227	3549	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	88.0043	2167	3549	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	87.941	2231	3549	95	below_threshold
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	87.8243	2260	3549	95	below_threshold
Lentzea fradiae	strain=CGMCC 4.3506	GCA_900100955.1	200378	200378	type	True	86.8259	2027	3549	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.5345	1763	3549	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0196	1212	3549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:24,312] [INFO] DFAST Taxonomy check result was written to GCF_024171805.1_ASM2417180v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:24,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:24,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:24,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference/checkm_data
[2024-01-24 12:55:24,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:24,413] [INFO] Task started: CheckM
[2024-01-24 12:55:24,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171805.1_ASM2417180v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171805.1_ASM2417180v1_genomic.fna/checkm_input GCF_024171805.1_ASM2417180v1_genomic.fna/checkm_result
[2024-01-24 12:58:20,708] [INFO] Task succeeded: CheckM
[2024-01-24 12:58:20,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:58:20,740] [INFO] ===== Completeness check finished =====
[2024-01-24 12:58:20,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:58:20,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171805.1_ASM2417180v1_genomic.fna/markers.fasta)
[2024-01-24 12:58:20,741] [INFO] Task started: Blastn
[2024-01-24 12:58:20,742] [INFO] Running command: blastn -query GCF_024171805.1_ASM2417180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg734aed4e-5fae-4e48-8cf8-9c8b484d7e2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171805.1_ASM2417180v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:23,001] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:23,006] [INFO] Selected 15 target genomes.
[2024-01-24 12:58:23,007] [INFO] Target genome list was writen to GCF_024171805.1_ASM2417180v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:58:23,030] [INFO] Task started: fastANI
[2024-01-24 12:58:23,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ee4428-bffc-494e-b4a7-b7a8f07899de/GCF_024171805.1_ASM2417180v1_genomic.fna.gz --refList GCF_024171805.1_ASM2417180v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171805.1_ASM2417180v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:00,233] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:00,249] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:00,249] [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_000974445.1	s__Lentzea aerocolonigenes	99.9938	3490	3549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_012184385.1	s__Lentzea indica	89.3995	2308	3549	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	89.1553	2444	3549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150765.1	s__Lentzea kentuckyensis	89.1261	2381	3549	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	89.0415	2347	3549	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	88.9289	2407	3549	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	88.7737	2523	3549	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	88.7288	2314	3549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	88.2273	2192	3549	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	88.0081	2167	3549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	87.9985	2025	3549	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	87.9697	2226	3549	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	87.8294	2260	3549	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	87.7437	2030	3549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100955.1	s__Lentzea fradiae	86.8325	2026	3549	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 12:59:00,256] [INFO] GTDB search result was written to GCF_024171805.1_ASM2417180v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:00,257] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:00,262] [INFO] DFAST_QC result json was written to GCF_024171805.1_ASM2417180v1_genomic.fna/dqc_result.json
[2024-01-24 12:59:00,262] [INFO] DFAST_QC completed!
[2024-01-24 12:59:00,262] [INFO] Total running time: 0h4m55s