[2024-01-24 13:22:11,449] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference
[2024-01-24 13:22:13,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,356] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a17b0e4-b5d3-4852-888e-099b87889282/GCF_000744705.1_ASM74470v1_genomic.fna.gz | prodigal -d GCF_000744705.1_ASM74470v1_genomic.fna/cds.fna -a GCF_000744705.1_ASM74470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:44,691] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:44,691] [INFO] Task started: HMMsearch
[2024-01-24 13:22:44,691] [INFO] Running command: hmmsearch --tblout GCF_000744705.1_ASM74470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference/reference_markers.hmm GCF_000744705.1_ASM74470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:45,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:45,228] [INFO] Found 6/6 markers.
[2024-01-24 13:22:45,297] [INFO] Query marker FASTA was written to GCF_000744705.1_ASM74470v1_genomic.fna/markers.fasta
[2024-01-24 13:22:45,297] [INFO] Task started: Blastn
[2024-01-24 13:22:45,297] [INFO] Running command: blastn -query GCF_000744705.1_ASM74470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference/reference_markers.fasta -out GCF_000744705.1_ASM74470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:46,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:46,589] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:46,589] [INFO] Target genome list was writen to GCF_000744705.1_ASM74470v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:46,594] [INFO] Task started: fastANI
[2024-01-24 13:22:46,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a17b0e4-b5d3-4852-888e-099b87889282/GCF_000744705.1_ASM74470v1_genomic.fna.gz --refList GCF_000744705.1_ASM74470v1_genomic.fna/target_genomes.txt --output GCF_000744705.1_ASM74470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:22,628] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:22,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:22,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:22,638] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:22,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:22,639] [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
Streptacidiphilus albus	strain=JL83	GCA_000744705.1	105425	105425	type	True	100.0	3303	3305	95	conclusive
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	99.9493	3128	3305	95	conclusive
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	83.2044	1477	3305	95	below_threshold
Streptacidiphilus rugosus	strain=AM-16	GCA_000744655.1	405783	405783	type	True	81.4192	1462	3305	95	below_threshold
Streptacidiphilus fuscans	strain=NEAU-YB345	GCA_015690355.1	2789292	2789292	type	True	81.3792	1444	3305	95	below_threshold
Streptacidiphilus pinicola	strain=MMS16-CNU450	GCA_003258295.1	2219663	2219663	type	True	81.095	1342	3305	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	80.9155	1485	3305	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	80.8601	1512	3305	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	80.7869	1452	3305	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	80.3969	1196	3305	95	below_threshold
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	80.2181	1070	3305	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	80.144	1406	3305	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	79.9915	1249	3305	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	79.9692	1393	3305	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	78.8574	917	3305	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	78.6994	907	3305	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	78.1904	910	3305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:22,640] [INFO] DFAST Taxonomy check result was written to GCF_000744705.1_ASM74470v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:22,640] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:22,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:22,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference/checkm_data
[2024-01-24 13:23:22,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:22,729] [INFO] Task started: CheckM
[2024-01-24 13:23:22,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000744705.1_ASM74470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000744705.1_ASM74470v1_genomic.fna/checkm_input GCF_000744705.1_ASM74470v1_genomic.fna/checkm_result
[2024-01-24 13:26:02,590] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:02,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:02,613] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:02,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:02,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000744705.1_ASM74470v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:02,613] [INFO] Task started: Blastn
[2024-01-24 13:26:02,613] [INFO] Running command: blastn -query GCF_000744705.1_ASM74470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefecf3c5-3bb9-4266-81e4-a23269e3acaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000744705.1_ASM74470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:04,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:04,665] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:04,665] [INFO] Target genome list was writen to GCF_000744705.1_ASM74470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:04,671] [INFO] Task started: fastANI
[2024-01-24 13:26:04,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a17b0e4-b5d3-4852-888e-099b87889282/GCF_000744705.1_ASM74470v1_genomic.fna.gz --refList GCF_000744705.1_ASM74470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000744705.1_ASM74470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:35,387] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:35,395] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:35,395] [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_000744705.1	s__Streptacidiphilus albus	100.0	3304	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014084125.1	s__Streptacidiphilus sp014084125	85.4948	1672	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084105.1	s__Streptacidiphilus sp014084105	84.8768	1820	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014284505.1	s__Streptacidiphilus sp014284505	84.3494	1771	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719095.1	s__Streptacidiphilus jeojiense	83.2684	1565	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751325.1	s__Streptacidiphilus sp003751325	83.2585	1568	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365705.1	s__Streptacidiphilus sp004365705	83.2018	1520	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787775.1	s__Streptacidiphilus carbonis	83.1549	1486	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744655.1	s__Streptacidiphilus rugosus	81.3891	1472	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690355.1	s__Streptacidiphilus fuscans	81.3798	1441	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258295.1	s__Streptacidiphilus pinicola	81.1184	1339	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	80.9129	1487	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000787835.1	s__Streptacidiphilus melanogenes	80.7663	1456	3305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:35,397] [INFO] GTDB search result was written to GCF_000744705.1_ASM74470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:35,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:35,400] [INFO] DFAST_QC result json was written to GCF_000744705.1_ASM74470v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:35,400] [INFO] DFAST_QC completed!
[2024-01-24 13:26:35,400] [INFO] Total running time: 0h4m24s