[2024-01-24 14:20:00,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:00,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:00,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference
[2024-01-24 14:20:02,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,154] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,155] [INFO] Running command: gunzip -c /var/lib/cwl/stgc215a823-4426-4d17-b432-b9365a2f2787/GCF_009742705.1_ASM974270v1_genomic.fna.gz | prodigal -d GCF_009742705.1_ASM974270v1_genomic.fna/cds.fna -a GCF_009742705.1_ASM974270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:12,469] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:12,469] [INFO] Task started: HMMsearch
[2024-01-24 14:20:12,469] [INFO] Running command: hmmsearch --tblout GCF_009742705.1_ASM974270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference/reference_markers.hmm GCF_009742705.1_ASM974270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:12,750] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:12,751] [INFO] Found 6/6 markers.
[2024-01-24 14:20:12,787] [INFO] Query marker FASTA was written to GCF_009742705.1_ASM974270v1_genomic.fna/markers.fasta
[2024-01-24 14:20:12,788] [INFO] Task started: Blastn
[2024-01-24 14:20:12,788] [INFO] Running command: blastn -query GCF_009742705.1_ASM974270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference/reference_markers.fasta -out GCF_009742705.1_ASM974270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:13,970] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:13,975] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:13,975] [INFO] Target genome list was writen to GCF_009742705.1_ASM974270v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:14,006] [INFO] Task started: fastANI
[2024-01-24 14:20:14,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgc215a823-4426-4d17-b432-b9365a2f2787/GCF_009742705.1_ASM974270v1_genomic.fna.gz --refList GCF_009742705.1_ASM974270v1_genomic.fna/target_genomes.txt --output GCF_009742705.1_ASM974270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:27,598] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:27,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:27,614] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:27,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:27,614] [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
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	99.9993	1254	1260	95	conclusive
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	84.4049	946	1260	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	83.8126	734	1260	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	83.7061	873	1260	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.5783	477	1260	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	78.5643	528	1260	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	78.1272	483	1260	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	78.1238	431	1260	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	77.6645	398	1260	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	77.269	376	1260	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.2571	471	1260	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.1881	408	1260	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	77.1579	371	1260	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	76.9914	381	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,616] [INFO] DFAST Taxonomy check result was written to GCF_009742705.1_ASM974270v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:27,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:27,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:27,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference/checkm_data
[2024-01-24 14:20:27,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:27,655] [INFO] Task started: CheckM
[2024-01-24 14:20:27,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009742705.1_ASM974270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009742705.1_ASM974270v1_genomic.fna/checkm_input GCF_009742705.1_ASM974270v1_genomic.fna/checkm_result
[2024-01-24 14:21:23,205] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:23,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:23,240] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:23,240] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:23,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009742705.1_ASM974270v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:23,241] [INFO] Task started: Blastn
[2024-01-24 14:21:23,241] [INFO] Running command: blastn -query GCF_009742705.1_ASM974270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg939ccb80-5b1d-4439-8bf5-b963229bef92/dqc_reference/reference_markers_gtdb.fasta -out GCF_009742705.1_ASM974270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:25,108] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:25,113] [INFO] Selected 15 target genomes.
[2024-01-24 14:21:25,113] [INFO] Target genome list was writen to GCF_009742705.1_ASM974270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:25,124] [INFO] Task started: fastANI
[2024-01-24 14:21:25,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgc215a823-4426-4d17-b432-b9365a2f2787/GCF_009742705.1_ASM974270v1_genomic.fna.gz --refList GCF_009742705.1_ASM974270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009742705.1_ASM974270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:38,581] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:38,596] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:38,596] [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_009742705.1	s__Auraticoccus cholistanensis	99.9993	1254	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101785.1	s__Auraticoccus monumenti	84.3966	947	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	83.8516	730	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_017876495.1	s__Friedmanniella capsulata	79.0296	637	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	78.8782	591	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105785.1	s__Friedmanniella sagamiharensis	78.5786	526	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362375.1	s__Enemella evansiae	78.5005	478	1260	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	78.3804	428	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_013408315.1	s__Microlunatus_A terrae	78.3093	528	1260	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_014193425.1	s__Friedmanniella antarctica	78.1424	481	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408305.1	s__Naumannella cuiyingiana	78.1246	431	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907175.1	s__Friedmanniella spumicola	78.0961	531	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	77.6805	349	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	77.581	453	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024345.1	s__Kribbella flavida	77.3003	478	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:38,598] [INFO] GTDB search result was written to GCF_009742705.1_ASM974270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:38,598] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:38,602] [INFO] DFAST_QC result json was written to GCF_009742705.1_ASM974270v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:38,602] [INFO] DFAST_QC completed!
[2024-01-24 14:21:38,602] [INFO] Total running time: 0h1m38s