[2024-01-25 19:32:35,780] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:35,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:35,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference
[2024-01-25 19:32:36,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:36,922] [INFO] Task started: Prodigal
[2024-01-25 19:32:36,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg03e17a5a-1e64-4029-8b57-930b7c1ca73c/GCF_021129235.1_ASM2112923v1_genomic.fna.gz | prodigal -d GCF_021129235.1_ASM2112923v1_genomic.fna/cds.fna -a GCF_021129235.1_ASM2112923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:58,487] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:58,487] [INFO] Task started: HMMsearch
[2024-01-25 19:32:58,487] [INFO] Running command: hmmsearch --tblout GCF_021129235.1_ASM2112923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference/reference_markers.hmm GCF_021129235.1_ASM2112923v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:58,782] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:58,783] [INFO] Found 6/6 markers.
[2024-01-25 19:32:58,840] [INFO] Query marker FASTA was written to GCF_021129235.1_ASM2112923v1_genomic.fna/markers.fasta
[2024-01-25 19:32:58,840] [INFO] Task started: Blastn
[2024-01-25 19:32:58,840] [INFO] Running command: blastn -query GCF_021129235.1_ASM2112923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference/reference_markers.fasta -out GCF_021129235.1_ASM2112923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:59,997] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:00,000] [INFO] Selected 17 target genomes.
[2024-01-25 19:33:00,000] [INFO] Target genome list was writen to GCF_021129235.1_ASM2112923v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:00,004] [INFO] Task started: fastANI
[2024-01-25 19:33:00,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg03e17a5a-1e64-4029-8b57-930b7c1ca73c/GCF_021129235.1_ASM2112923v1_genomic.fna.gz --refList GCF_021129235.1_ASM2112923v1_genomic.fna/target_genomes.txt --output GCF_021129235.1_ASM2112923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:21,613] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:21,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:21,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:21,627] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:21,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:21,628] [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
Kineosporia mesophila	strain=JCM 16902	GCA_021129235.1	566012	566012	type	True	100.0	2561	2564	95	conclusive
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	84.131	1667	2564	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	83.3255	1546	2564	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	77.1661	368	2564	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.9907	334	2564	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	76.902	326	2564	95	below_threshold
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	76.8512	471	2564	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.7352	349	2564	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	76.7054	493	2564	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	76.661	451	2564	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	76.6304	439	2564	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	76.6094	335	2564	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	76.5836	356	2564	95	below_threshold
Sporichthya polymorpha	strain=DSM 43042	GCA_000384115.1	35751	35751	type	True	76.4582	400	2564	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	76.3361	395	2564	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	76.2927	539	2564	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.2591	440	2564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:21,630] [INFO] DFAST Taxonomy check result was written to GCF_021129235.1_ASM2112923v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:21,632] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:21,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:21,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference/checkm_data
[2024-01-25 19:33:21,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:21,711] [INFO] Task started: CheckM
[2024-01-25 19:33:21,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021129235.1_ASM2112923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021129235.1_ASM2112923v1_genomic.fna/checkm_input GCF_021129235.1_ASM2112923v1_genomic.fna/checkm_result
[2024-01-25 19:34:36,946] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:36,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:36,966] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:36,966] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:36,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021129235.1_ASM2112923v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:36,967] [INFO] Task started: Blastn
[2024-01-25 19:34:36,967] [INFO] Running command: blastn -query GCF_021129235.1_ASM2112923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c370c12-721b-415c-afc5-94a7b030d66f/dqc_reference/reference_markers_gtdb.fasta -out GCF_021129235.1_ASM2112923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:38,818] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:38,824] [INFO] Selected 18 target genomes.
[2024-01-25 19:34:38,824] [INFO] Target genome list was writen to GCF_021129235.1_ASM2112923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:38,834] [INFO] Task started: fastANI
[2024-01-25 19:34:38,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg03e17a5a-1e64-4029-8b57-930b7c1ca73c/GCF_021129235.1_ASM2112923v1_genomic.fna.gz --refList GCF_021129235.1_ASM2112923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021129235.1_ASM2112923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:59,077] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:59,088] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:34:59,088] [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_018499875.1	s__Kineosporia sp018499875	84.1184	1668	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000719025.1	s__Kineosporia aurantiaca	83.0357	1563	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	77.5731	427	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198675.1	s__R-H-3 sp002198675	77.3721	611	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794595.1	s__JADJPO01 sp016794595	77.2733	474	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213575.1	s__R-H-3 sp016213575	77.2643	489	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198655.1	s__R-H-3 sp002198655	77.2518	594	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	77.2231	424	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_003721155.3	s__Marihabitans melonis	77.1276	312	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCA_014360395.1	s__Actinotalea sp014360395	77.0873	215	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719445.1	s__JAAYAH01 sp012719445	76.8916	406	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JAAYAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426185.1	s__Cellulomonas sp000426185	76.8724	328	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011839805.1	s__Kineococcus rubinsiae	76.848	471	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017305.1	s__Kineococcus radiotolerans	76.7037	492	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	98.46	98.46	0.90	0.90	2	-
GCF_001270745.1	s__Jiangella muralis	76.2883	542	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716785.1	s__Thermopolyspora flexuosa	76.2547	447	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000518265.1	s__Spirillospora oligospora	76.2394	513	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	76.1086	562	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:59,091] [INFO] GTDB search result was written to GCF_021129235.1_ASM2112923v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:59,092] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:59,095] [INFO] DFAST_QC result json was written to GCF_021129235.1_ASM2112923v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:59,095] [INFO] DFAST_QC completed!
[2024-01-25 19:34:59,095] [INFO] Total running time: 0h2m23s