[2024-01-24 14:46:57,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference
[2024-01-24 14:46:58,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,913] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,914] [INFO] Running command: gunzip -c /var/lib/cwl/stg33d863dd-9ca5-4a79-8968-451f0fdc0886/GCF_026642255.1_ASM2664225v1_genomic.fna.gz | prodigal -d GCF_026642255.1_ASM2664225v1_genomic.fna/cds.fna -a GCF_026642255.1_ASM2664225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:22,002] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:22,003] [INFO] Task started: HMMsearch
[2024-01-24 14:47:22,003] [INFO] Running command: hmmsearch --tblout GCF_026642255.1_ASM2664225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference/reference_markers.hmm GCF_026642255.1_ASM2664225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:22,396] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:22,398] [INFO] Found 6/6 markers.
[2024-01-24 14:47:22,456] [INFO] Query marker FASTA was written to GCF_026642255.1_ASM2664225v1_genomic.fna/markers.fasta
[2024-01-24 14:47:22,457] [INFO] Task started: Blastn
[2024-01-24 14:47:22,457] [INFO] Running command: blastn -query GCF_026642255.1_ASM2664225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference/reference_markers.fasta -out GCF_026642255.1_ASM2664225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:23,842] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:23,847] [INFO] Selected 18 target genomes.
[2024-01-24 14:47:23,847] [INFO] Target genome list was writen to GCF_026642255.1_ASM2664225v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:23,860] [INFO] Task started: fastANI
[2024-01-24 14:47:23,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg33d863dd-9ca5-4a79-8968-451f0fdc0886/GCF_026642255.1_ASM2664225v1_genomic.fna.gz --refList GCF_026642255.1_ASM2664225v1_genomic.fna/target_genomes.txt --output GCF_026642255.1_ASM2664225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:53,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:53,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:53,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:53,417] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:53,418] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:53,418] [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
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	85.8114	1638	2422	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	85.7706	1406	2422	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	85.7558	1650	2422	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	85.7555	1577	2422	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	85.6338	1661	2422	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	85.5874	1659	2422	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	85.4087	1504	2422	95	below_threshold
Nocardiopsis quinghaiensis	strain=YIM 28A4	GCA_008638365.1	464995	464995	type	True	85.3429	1411	2422	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	84.9392	1368	2422	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	83.4125	1370	2422	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	83.3785	1376	2422	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	83.356	1476	2422	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	81.9593	1195	2422	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.3074	1006	2422	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.343	805	2422	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.2803	844	2422	95	below_threshold
Actinocorallia herbida	strain=DSM 44254	GCA_003751225.1	58109	58109	type	True	76.8339	720	2422	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	76.5136	407	2422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:53,425] [INFO] DFAST Taxonomy check result was written to GCF_026642255.1_ASM2664225v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:53,426] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:53,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:53,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference/checkm_data
[2024-01-24 14:47:53,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:53,500] [INFO] Task started: CheckM
[2024-01-24 14:47:53,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026642255.1_ASM2664225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026642255.1_ASM2664225v1_genomic.fna/checkm_input GCF_026642255.1_ASM2664225v1_genomic.fna/checkm_result
[2024-01-24 14:49:55,113] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:55,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:55,142] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:55,142] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:55,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026642255.1_ASM2664225v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:55,143] [INFO] Task started: Blastn
[2024-01-24 14:49:55,143] [INFO] Running command: blastn -query GCF_026642255.1_ASM2664225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52183548-75a0-419f-ad67-b6c3c61dffc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_026642255.1_ASM2664225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:57,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:57,344] [INFO] Selected 15 target genomes.
[2024-01-24 14:49:57,344] [INFO] Target genome list was writen to GCF_026642255.1_ASM2664225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:57,355] [INFO] Task started: fastANI
[2024-01-24 14:49:57,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg33d863dd-9ca5-4a79-8968-451f0fdc0886/GCF_026642255.1_ASM2664225v1_genomic.fna.gz --refList GCF_026642255.1_ASM2664225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026642255.1_ASM2664225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:24,543] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:24,560] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:50:24,560] [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_000092985.1	s__Nocardiopsis dassonvillei	85.8328	1635	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCA_002529455.1	s__Nocardiopsis fusca	85.7733	1611	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905145.1	s__Nocardiopsis sp001905145	85.6125	1471	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396365.1	s__Nocardiopsis alborubida	85.559	1665	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_008638365.1	s__Nocardiopsis quinghaiensis	85.3254	1414	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	85.2938	1501	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_009830945.1	s__Nocardiopsis sp009830945	85.0571	1424	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_000341065.1	s__Nocardiopsis halotolerans	84.953	1366	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	83.3363	1480	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	83.331	1377	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634495.1	s__Nocardiopsis sp003634495	83.2845	1479	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386285.1	s__Nocardiopsis sp003386285	83.1993	1261	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	82.8823	1051	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892575.1	s__Nocardiopsis coralli	81.9716	1193	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	79.5385	1115	2422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:24,562] [INFO] GTDB search result was written to GCF_026642255.1_ASM2664225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:24,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:24,566] [INFO] DFAST_QC result json was written to GCF_026642255.1_ASM2664225v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:24,566] [INFO] DFAST_QC completed!
[2024-01-24 14:50:24,566] [INFO] Total running time: 0h3m27s