[2024-01-24 13:17:42,036] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:42,038] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:42,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference
[2024-01-24 13:17:43,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:43,233] [INFO] Task started: Prodigal
[2024-01-24 13:17:43,233] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c14278f-587a-4b15-b4b8-fc53d3c15e7c/GCF_006716235.1_ASM671623v1_genomic.fna.gz | prodigal -d GCF_006716235.1_ASM671623v1_genomic.fna/cds.fna -a GCF_006716235.1_ASM671623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:52,955] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:52,956] [INFO] Task started: HMMsearch
[2024-01-24 13:17:52,956] [INFO] Running command: hmmsearch --tblout GCF_006716235.1_ASM671623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference/reference_markers.hmm GCF_006716235.1_ASM671623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:53,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:53,220] [INFO] Found 6/6 markers.
[2024-01-24 13:17:53,250] [INFO] Query marker FASTA was written to GCF_006716235.1_ASM671623v1_genomic.fna/markers.fasta
[2024-01-24 13:17:53,250] [INFO] Task started: Blastn
[2024-01-24 13:17:53,250] [INFO] Running command: blastn -query GCF_006716235.1_ASM671623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference/reference_markers.fasta -out GCF_006716235.1_ASM671623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:54,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:54,171] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:54,172] [INFO] Target genome list was writen to GCF_006716235.1_ASM671623v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:54,252] [INFO] Task started: fastANI
[2024-01-24 13:17:54,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c14278f-587a-4b15-b4b8-fc53d3c15e7c/GCF_006716235.1_ASM671623v1_genomic.fna.gz --refList GCF_006716235.1_ASM671623v1_genomic.fna/target_genomes.txt --output GCF_006716235.1_ASM671623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:08,797] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:08,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:08,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:08,812] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:08,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:08,813] [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
Propioniferax innocua	strain=DSM 8251	GCA_006716235.1	1753	1753	type	True	100.0	926	927	95	conclusive
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	77.8607	233	927	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	77.7057	223	927	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.5484	178	927	95	below_threshold
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	77.52	192	927	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	77.4942	193	927	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.4131	177	927	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.4109	176	927	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.2848	161	927	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.0794	156	927	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	77.0269	89	927	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	76.7056	142	927	95	below_threshold
Streptomyces lydicus	strain=ATCC 25470	GCA_004125245.1	47763	47763	suspected-type	True	76.5225	112	927	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	76.5105	97	927	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	76.343	159	927	95	below_threshold
Streptomyces lydicus	strain=NRRL ISP-5461	GCA_000717345.1	47763	47763	suspected-type	True	76.3047	114	927	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	76.1941	131	927	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	75.9707	100	927	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	75.932	126	927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:08,814] [INFO] DFAST Taxonomy check result was written to GCF_006716235.1_ASM671623v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:08,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:08,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:08,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference/checkm_data
[2024-01-24 13:18:08,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:08,849] [INFO] Task started: CheckM
[2024-01-24 13:18:08,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716235.1_ASM671623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716235.1_ASM671623v1_genomic.fna/checkm_input GCF_006716235.1_ASM671623v1_genomic.fna/checkm_result
[2024-01-24 13:19:17,351] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:17,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:17,372] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:17,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:17,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716235.1_ASM671623v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:17,373] [INFO] Task started: Blastn
[2024-01-24 13:19:17,373] [INFO] Running command: blastn -query GCF_006716235.1_ASM671623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e9a65e7-a46e-4802-b0fb-477cae39749c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716235.1_ASM671623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:18,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:18,736] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:18,736] [INFO] Target genome list was writen to GCF_006716235.1_ASM671623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:18,798] [INFO] Task started: fastANI
[2024-01-24 13:19:18,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c14278f-587a-4b15-b4b8-fc53d3c15e7c/GCF_006716235.1_ASM671623v1_genomic.fna.gz --refList GCF_006716235.1_ASM671623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716235.1_ASM671623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:29,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:29,859] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:29,859] [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_006716235.1	s__Propioniferax innocua	100.0	926	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniferax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004362375.1	s__Enemella evansiae	77.9174	240	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCA_002250625.1	s__Enemella sp002250625	77.7057	223	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_000423085.1	s__Granulicoccus phenolivorans	77.4942	193	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Granulicoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900101785.1	s__Auraticoccus monumenti	77.4736	178	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742705.1	s__Auraticoccus cholistanensis	77.4131	177	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900092135.1	s__Raineyella antarctica	77.3888	167	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.2848	161	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCA_012839035.1	s__Enemella sp012839035	77.1519	155	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408305.1	s__Naumannella cuiyingiana	77.0955	155	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	76.7524	160	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	76.6798	143	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	76.6359	145	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882685.1	s__Propionicimonas sp017882685	76.4595	95	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	76.4192	99	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	76.2471	130	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:29,861] [INFO] GTDB search result was written to GCF_006716235.1_ASM671623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:29,862] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:29,866] [INFO] DFAST_QC result json was written to GCF_006716235.1_ASM671623v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:29,866] [INFO] DFAST_QC completed!
[2024-01-24 13:19:29,866] [INFO] Total running time: 0h1m48s