[2024-01-24 14:31:28,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,794] [INFO] DQC Reference Directory: /var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference
[2024-01-24 14:31:29,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:29,874] [INFO] Task started: Prodigal
[2024-01-24 14:31:29,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg14c67214-d2b6-4ce5-bd72-f723033a66ab/GCF_009664835.1_ASM966483v1_genomic.fna.gz | prodigal -d GCF_009664835.1_ASM966483v1_genomic.fna/cds.fna -a GCF_009664835.1_ASM966483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:43,081] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:43,081] [INFO] Task started: HMMsearch
[2024-01-24 14:31:43,081] [INFO] Running command: hmmsearch --tblout GCF_009664835.1_ASM966483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference/reference_markers.hmm GCF_009664835.1_ASM966483v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:43,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:43,287] [INFO] Found 6/6 markers.
[2024-01-24 14:31:43,322] [INFO] Query marker FASTA was written to GCF_009664835.1_ASM966483v1_genomic.fna/markers.fasta
[2024-01-24 14:31:43,322] [INFO] Task started: Blastn
[2024-01-24 14:31:43,323] [INFO] Running command: blastn -query GCF_009664835.1_ASM966483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference/reference_markers.fasta -out GCF_009664835.1_ASM966483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:44,589] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:44,592] [INFO] Selected 24 target genomes.
[2024-01-24 14:31:44,592] [INFO] Target genome list was writen to GCF_009664835.1_ASM966483v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:44,602] [INFO] Task started: fastANI
[2024-01-24 14:31:44,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c67214-d2b6-4ce5-bd72-f723033a66ab/GCF_009664835.1_ASM966483v1_genomic.fna.gz --refList GCF_009664835.1_ASM966483v1_genomic.fna/target_genomes.txt --output GCF_009664835.1_ASM966483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:13,378] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:13,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:13,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:13,392] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:32:13,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:32:13,392] [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
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	80.0557	828	1610	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.9944	818	1610	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	79.943	778	1610	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	79.8831	798	1610	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	79.8085	786	1610	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	79.7585	787	1610	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	79.7513	764	1610	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	79.7191	701	1610	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	79.7005	792	1610	95	below_threshold
Saccharopolyspora phatthalungensis	strain=DSM 45584	GCA_014203395.1	664693	664693	type	True	79.6453	659	1610	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	79.6068	794	1610	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	79.5596	710	1610	95	below_threshold
Saccharopolyspora dendranthemae	strain=DSM 46699	GCA_007829955.1	1181886	1181886	type	True	79.5094	734	1610	95	below_threshold
Actinopolyspora saharensis	strain=DSM 45459	GCA_900100925.1	995062	995062	type	True	78.7018	505	1610	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	78.5349	471	1610	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	78.4364	518	1610	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.2296	501	1610	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	78.1518	501	1610	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	77.6471	458	1610	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	77.5959	469	1610	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	77.5062	467	1610	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	77.4192	399	1610	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	76.4269	279	1610	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	76.0989	442	1610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:13,393] [INFO] DFAST Taxonomy check result was written to GCF_009664835.1_ASM966483v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:13,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:13,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:13,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference/checkm_data
[2024-01-24 14:32:13,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:13,440] [INFO] Task started: CheckM
[2024-01-24 14:32:13,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009664835.1_ASM966483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009664835.1_ASM966483v1_genomic.fna/checkm_input GCF_009664835.1_ASM966483v1_genomic.fna/checkm_result
[2024-01-24 14:33:31,303] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:31,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:31,317] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:31,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:31,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009664835.1_ASM966483v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:31,317] [INFO] Task started: Blastn
[2024-01-24 14:33:31,317] [INFO] Running command: blastn -query GCF_009664835.1_ASM966483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4230091-4071-45bc-94cd-93bc01936201/dqc_reference/reference_markers_gtdb.fasta -out GCF_009664835.1_ASM966483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:32,930] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:32,932] [INFO] Selected 20 target genomes.
[2024-01-24 14:33:32,933] [INFO] Target genome list was writen to GCF_009664835.1_ASM966483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:32,942] [INFO] Task started: fastANI
[2024-01-24 14:33:32,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c67214-d2b6-4ce5-bd72-f723033a66ab/GCF_009664835.1_ASM966483v1_genomic.fna.gz --refList GCF_009664835.1_ASM966483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009664835.1_ASM966483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:58,598] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:58,610] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:58,610] [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_009664835.1	s__Allosaccharopolyspora coralli	100.0	1606	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000062885.1	s__Saccharopolyspora_D erythraea	80.0438	814	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	99.99	99.99	1.00	1.00	5	-
GCF_014203325.1	s__Saccharopolyspora_C gloriosae	80.0392	773	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	80.0109	818	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016526145.1	s__Saccharopolyspora_C sp016526145	79.8832	774	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	79.8198	783	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	79.7774	786	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_014646075.1	s__Saccharopolyspora subtropica	79.7385	698	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	79.7379	766	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112555.1	s__Saccharopolyspora jiangxiensis	79.6663	780	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	99.99	1.00	1.00	3	-
GCF_014697215.1	s__Saccharopolyspora pogona	79.6184	747	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	79.6147	793	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829955.1	s__Saccharopolyspora dendranthemae	79.5356	730	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209505.1	s__Saccharopolyspora sp015209505	79.5226	578	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100925.1	s__Actinopolyspora saharensis	78.7284	503	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_900116555.1	s__Actinopolyspora righensis	78.5352	471	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
GCF_900104475.1	s__Actinopolyspora xinjiangensis	78.4593	515	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	78.2595	497	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796545.1	s__Amycolatopsis sp002796545	77.8191	465	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014647895.1	s__Pilimelia anulata	76.4345	278	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:58,611] [INFO] GTDB search result was written to GCF_009664835.1_ASM966483v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:58,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:58,615] [INFO] DFAST_QC result json was written to GCF_009664835.1_ASM966483v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:58,615] [INFO] DFAST_QC completed!
[2024-01-24 14:33:58,615] [INFO] Total running time: 0h2m30s