[2024-01-25 20:18:21,072] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:21,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:21,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference
[2024-01-25 20:18:22,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,236] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg884b5d39-c06b-4905-b750-62010ddc9a4a/GCF_003634705.1_ASM363470v1_genomic.fna.gz | prodigal -d GCF_003634705.1_ASM363470v1_genomic.fna/cds.fna -a GCF_003634705.1_ASM363470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:42,023] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:42,024] [INFO] Task started: HMMsearch
[2024-01-25 20:18:42,024] [INFO] Running command: hmmsearch --tblout GCF_003634705.1_ASM363470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference/reference_markers.hmm GCF_003634705.1_ASM363470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:42,350] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:42,351] [INFO] Found 6/6 markers.
[2024-01-25 20:18:42,411] [INFO] Query marker FASTA was written to GCF_003634705.1_ASM363470v1_genomic.fna/markers.fasta
[2024-01-25 20:18:42,411] [INFO] Task started: Blastn
[2024-01-25 20:18:42,411] [INFO] Running command: blastn -query GCF_003634705.1_ASM363470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference/reference_markers.fasta -out GCF_003634705.1_ASM363470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:43,595] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:43,597] [INFO] Selected 16 target genomes.
[2024-01-25 20:18:43,597] [INFO] Target genome list was writen to GCF_003634705.1_ASM363470v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:43,611] [INFO] Task started: fastANI
[2024-01-25 20:18:43,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg884b5d39-c06b-4905-b750-62010ddc9a4a/GCF_003634705.1_ASM363470v1_genomic.fna.gz --refList GCF_003634705.1_ASM363470v1_genomic.fna/target_genomes.txt --output GCF_003634705.1_ASM363470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:19,507] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:19,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:19,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:19,517] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:19,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:19,518] [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
Actinomadura pelletieri	strain=DSM 43383	GCA_003634705.1	111805	111805	type	True	100.0	2500	2501	95	conclusive
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	94.0687	2184	2501	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	86.8359	1590	2501	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	85.0443	1720	2501	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	85.0158	1685	2501	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	84.8874	1715	2501	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	84.6302	1399	2501	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	84.4786	1448	2501	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	84.3665	1506	2501	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	84.3156	1533	2501	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	84.3146	1548	2501	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	84.3007	1367	2501	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.213	1518	2501	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.0229	1549	2501	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.7665	1205	2501	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.604	1174	2501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:19,525] [INFO] DFAST Taxonomy check result was written to GCF_003634705.1_ASM363470v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:19,525] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:19,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:19,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference/checkm_data
[2024-01-25 20:19:19,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:19,609] [INFO] Task started: CheckM
[2024-01-25 20:19:19,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634705.1_ASM363470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634705.1_ASM363470v1_genomic.fna/checkm_input GCF_003634705.1_ASM363470v1_genomic.fna/checkm_result
[2024-01-25 20:20:33,642] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:33,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:33,665] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:33,665] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:33,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634705.1_ASM363470v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:33,666] [INFO] Task started: Blastn
[2024-01-25 20:20:33,666] [INFO] Running command: blastn -query GCF_003634705.1_ASM363470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8764c2cc-cedc-4b80-a22c-38567e0301e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634705.1_ASM363470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:35,614] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:35,617] [INFO] Selected 13 target genomes.
[2024-01-25 20:20:35,617] [INFO] Target genome list was writen to GCF_003634705.1_ASM363470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:35,650] [INFO] Task started: fastANI
[2024-01-25 20:20:35,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg884b5d39-c06b-4905-b750-62010ddc9a4a/GCF_003634705.1_ASM363470v1_genomic.fna.gz --refList GCF_003634705.1_ASM363470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634705.1_ASM363470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:05,258] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:05,270] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:05,270] [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_003634705.1	s__Spirillospora pelletieri	100.0	2500	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003432485.1	s__Spirillospora sp003432485	94.0777	2182	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889715.1	s__Spirillospora sp005889715	86.822	1592	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	86.8103	1568	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348735.1	s__Spirillospora sp004348735	86.7324	1656	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552135.1	s__Spirillospora chibensis	84.9963	1690	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004349235.1	s__Spirillospora darangshiensis	84.5144	1444	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	84.4968	1609	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	84.4756	1243	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	84.4446	1572	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	84.327	1546	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	84.1148	1561	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659615.1	s__Spirillospora fibrosa	82.8495	1400	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:05,272] [INFO] GTDB search result was written to GCF_003634705.1_ASM363470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:05,273] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:05,278] [INFO] DFAST_QC result json was written to GCF_003634705.1_ASM363470v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:05,279] [INFO] DFAST_QC completed!
[2024-01-25 20:21:05,279] [INFO] Total running time: 0h2m44s