[2024-01-24 11:59:11,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:11,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:11,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference
[2024-01-24 11:59:12,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:12,477] [INFO] Task started: Prodigal
[2024-01-24 11:59:12,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg32f45af7-1399-48da-b731-50d9fee1c630/GCF_017876495.1_ASM1787649v1_genomic.fna.gz | prodigal -d GCF_017876495.1_ASM1787649v1_genomic.fna/cds.fna -a GCF_017876495.1_ASM1787649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:24,101] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:24,102] [INFO] Task started: HMMsearch
[2024-01-24 11:59:24,102] [INFO] Running command: hmmsearch --tblout GCF_017876495.1_ASM1787649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference/reference_markers.hmm GCF_017876495.1_ASM1787649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:24,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:24,442] [INFO] Found 6/6 markers.
[2024-01-24 11:59:24,502] [INFO] Query marker FASTA was written to GCF_017876495.1_ASM1787649v1_genomic.fna/markers.fasta
[2024-01-24 11:59:24,503] [INFO] Task started: Blastn
[2024-01-24 11:59:24,503] [INFO] Running command: blastn -query GCF_017876495.1_ASM1787649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference/reference_markers.fasta -out GCF_017876495.1_ASM1787649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:25,906] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:25,910] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:25,910] [INFO] Target genome list was writen to GCF_017876495.1_ASM1787649v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:25,941] [INFO] Task started: fastANI
[2024-01-24 11:59:25,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg32f45af7-1399-48da-b731-50d9fee1c630/GCF_017876495.1_ASM1787649v1_genomic.fna.gz --refList GCF_017876495.1_ASM1787649v1_genomic.fna/target_genomes.txt --output GCF_017876495.1_ASM1787649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:45,050] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:45,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:45,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:45,063] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:45,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:45,064] [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
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	80.7323	825	1469	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	80.518	718	1469	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	80.3227	832	1469	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	79.9094	710	1469	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	79.2765	561	1469	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	79.1899	569	1469	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	79.1238	630	1469	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	79.0254	673	1469	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.9953	658	1469	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.9046	499	1469	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	78.6254	630	1469	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	78.276	660	1469	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.6751	526	1469	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.4009	453	1469	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	77.3625	472	1469	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	77.3316	526	1469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:45,077] [INFO] DFAST Taxonomy check result was written to GCF_017876495.1_ASM1787649v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:45,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:45,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:45,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference/checkm_data
[2024-01-24 11:59:45,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:45,122] [INFO] Task started: CheckM
[2024-01-24 11:59:45,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876495.1_ASM1787649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876495.1_ASM1787649v1_genomic.fna/checkm_input GCF_017876495.1_ASM1787649v1_genomic.fna/checkm_result
[2024-01-24 12:00:39,932] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:39,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:39,955] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:39,955] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:39,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876495.1_ASM1787649v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:39,956] [INFO] Task started: Blastn
[2024-01-24 12:00:39,956] [INFO] Running command: blastn -query GCF_017876495.1_ASM1787649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17070cf8-073a-43c3-be07-09c2d102cbd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876495.1_ASM1787649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:42,287] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:42,290] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:42,290] [INFO] Target genome list was writen to GCF_017876495.1_ASM1787649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:42,300] [INFO] Task started: fastANI
[2024-01-24 12:00:42,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg32f45af7-1399-48da-b731-50d9fee1c630/GCF_017876495.1_ASM1787649v1_genomic.fna.gz --refList GCF_017876495.1_ASM1787649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876495.1_ASM1787649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:56,476] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:56,494] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:56,494] [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_017876495.1	s__Friedmanniella capsulata	100.0	1469	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900105065.1	s__Friedmanniella luteola	87.6013	1196	1469	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	80.7426	823	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193425.1	s__Friedmanniella antarctica	80.5414	718	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907175.1	s__Friedmanniella spumicola	80.4021	829	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110855.1	s__Friedmanniella flava	80.3334	830	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	79.8756	714	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	79.1831	571	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_900101785.1	s__Auraticoccus monumenti	79.0332	672	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000270245.1	s__Microlunatus phosphovorus	78.8917	501	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805915.1	s__CADCUO01 sp902805915	78.7797	405	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__CADCUO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299835.1	s__Microlunatus_B speluncae	78.6183	631	1469	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_013407955.1	s__Microlunatus_B parietis	78.2698	660	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:56,496] [INFO] GTDB search result was written to GCF_017876495.1_ASM1787649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:56,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:56,500] [INFO] DFAST_QC result json was written to GCF_017876495.1_ASM1787649v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:56,500] [INFO] DFAST_QC completed!
[2024-01-24 12:00:56,500] [INFO] Total running time: 0h1m45s