[2024-01-24 12:07:06,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference
[2024-01-24 12:07:08,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:08,250] [INFO] Task started: Prodigal
[2024-01-24 12:07:08,250] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0a49567-2b57-4d20-9991-5b17461c3a21/GCF_001552335.1_ASM155233v1_genomic.fna.gz | prodigal -d GCF_001552335.1_ASM155233v1_genomic.fna/cds.fna -a GCF_001552335.1_ASM155233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:19,799] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:19,799] [INFO] Task started: HMMsearch
[2024-01-24 12:07:19,800] [INFO] Running command: hmmsearch --tblout GCF_001552335.1_ASM155233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference/reference_markers.hmm GCF_001552335.1_ASM155233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:20,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:20,131] [INFO] Found 6/6 markers.
[2024-01-24 12:07:20,171] [INFO] Query marker FASTA was written to GCF_001552335.1_ASM155233v1_genomic.fna/markers.fasta
[2024-01-24 12:07:20,172] [INFO] Task started: Blastn
[2024-01-24 12:07:20,172] [INFO] Running command: blastn -query GCF_001552335.1_ASM155233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference/reference_markers.fasta -out GCF_001552335.1_ASM155233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:21,292] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:21,298] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:21,298] [INFO] Target genome list was writen to GCF_001552335.1_ASM155233v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:21,304] [INFO] Task started: fastANI
[2024-01-24 12:07:21,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0a49567-2b57-4d20-9991-5b17461c3a21/GCF_001552335.1_ASM155233v1_genomic.fna.gz --refList GCF_001552335.1_ASM155233v1_genomic.fna/target_genomes.txt --output GCF_001552335.1_ASM155233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:33,905] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:33,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:33,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:33,919] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:33,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:33,919] [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
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	100.0	1330	1330	95	conclusive
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	99.9877	1299	1330	95	conclusive
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.8909	473	1330	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	78.8832	463	1330	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.666	281	1330	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.0574	317	1330	95	below_threshold
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	77.9934	349	1330	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.8987	377	1330	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.8822	339	1330	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.8396	343	1330	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	77.7266	236	1330	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	77.7156	338	1330	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	77.1733	372	1330	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	77.1088	227	1330	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.0021	240	1330	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	76.9133	281	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,921] [INFO] DFAST Taxonomy check result was written to GCF_001552335.1_ASM155233v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:33,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:33,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:33,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference/checkm_data
[2024-01-24 12:07:33,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:33,967] [INFO] Task started: CheckM
[2024-01-24 12:07:33,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552335.1_ASM155233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552335.1_ASM155233v1_genomic.fna/checkm_input GCF_001552335.1_ASM155233v1_genomic.fna/checkm_result
[2024-01-24 12:08:31,922] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:31,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:31,944] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:31,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:31,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552335.1_ASM155233v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:31,945] [INFO] Task started: Blastn
[2024-01-24 12:08:31,946] [INFO] Running command: blastn -query GCF_001552335.1_ASM155233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad58bd7-af34-4289-ad99-f74020c72903/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552335.1_ASM155233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:33,641] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:33,646] [INFO] Selected 18 target genomes.
[2024-01-24 12:08:33,646] [INFO] Target genome list was writen to GCF_001552335.1_ASM155233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:33,669] [INFO] Task started: fastANI
[2024-01-24 12:08:33,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0a49567-2b57-4d20-9991-5b17461c3a21/GCF_001552335.1_ASM155233v1_genomic.fna.gz --refList GCF_001552335.1_ASM155233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552335.1_ASM155233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:48,264] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:48,281] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:48,282] [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_000423085.1	s__Granulicoccus phenolivorans	99.9877	1299	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Granulicoccus	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCA_002250625.1	s__Enemella sp002250625	78.9018	461	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_004362375.1	s__Enemella evansiae	78.8613	460	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCF_003344635.1	s__Desertihabitans aurantiacus	78.0494	316	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_900092135.1	s__Raineyella antarctica	77.9931	349	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	77.8948	337	1330	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	77.8296	344	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	77.7355	336	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693855.1	s__Micropruina sp013693855	77.6938	258	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	77.6449	344	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007362775.1	s__Microlunatus_A sp007362775	77.5889	296	1330	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_012839035.1	s__Enemella sp012839035	77.5397	248	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105785.1	s__Friedmanniella sagamiharensis	77.4298	295	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715445.1	s__Avipropionibacterium avicola	77.3366	222	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Avipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105385.1	s__Microlunatus_A soli	77.335	329	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	77.2364	370	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407955.1	s__Microlunatus_B parietis	77.159	374	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531445.1	s__Pseudonocardia sp018531445	75.9472	326	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:48,283] [INFO] GTDB search result was written to GCF_001552335.1_ASM155233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:48,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:48,288] [INFO] DFAST_QC result json was written to GCF_001552335.1_ASM155233v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:48,288] [INFO] DFAST_QC completed!
[2024-01-24 12:08:48,288] [INFO] Total running time: 0h1m41s