[2024-01-25 17:52:05,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:05,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:05,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference
[2024-01-25 17:52:06,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:06,673] [INFO] Task started: Prodigal
[2024-01-25 17:52:06,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg9753847a-0f63-4695-9466-8bbe4c8f0f37/GCF_009299835.1_ASM929983v1_genomic.fna.gz | prodigal -d GCF_009299835.1_ASM929983v1_genomic.fna/cds.fna -a GCF_009299835.1_ASM929983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:22,852] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:22,853] [INFO] Task started: HMMsearch
[2024-01-25 17:52:22,853] [INFO] Running command: hmmsearch --tblout GCF_009299835.1_ASM929983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference/reference_markers.hmm GCF_009299835.1_ASM929983v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:23,158] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:23,159] [INFO] Found 6/6 markers.
[2024-01-25 17:52:23,212] [INFO] Query marker FASTA was written to GCF_009299835.1_ASM929983v1_genomic.fna/markers.fasta
[2024-01-25 17:52:23,213] [INFO] Task started: Blastn
[2024-01-25 17:52:23,213] [INFO] Running command: blastn -query GCF_009299835.1_ASM929983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference/reference_markers.fasta -out GCF_009299835.1_ASM929983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:24,385] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:24,389] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:24,390] [INFO] Target genome list was writen to GCF_009299835.1_ASM929983v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:24,419] [INFO] Task started: fastANI
[2024-01-25 17:52:24,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg9753847a-0f63-4695-9466-8bbe4c8f0f37/GCF_009299835.1_ASM929983v1_genomic.fna.gz --refList GCF_009299835.1_ASM929983v1_genomic.fna/target_genomes.txt --output GCF_009299835.1_ASM929983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:45,017] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:45,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:45,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:45,027] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:45,027] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:45,028] [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 speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	100.0	2254	2254	95	conclusive
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	83.8938	1582	2254	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	78.5579	664	2254	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	78.5572	563	2254	95	below_threshold
Microlunatus elymi	strain=KUDC0627	GCA_007362775.1	2596828	2596828	type	True	78.3045	626	2254	95	below_threshold
Microlunatus endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	77.9036	554	2254	95	below_threshold
Microlunatus soli	strain=DSM 21800	GCA_900105385.1	630515	630515	type	True	77.8907	777	2254	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.8898	506	2254	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.735	582	2254	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	77.5657	560	2254	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.447	531	2254	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.092	555	2254	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.0579	567	2254	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	76.955	521	2254	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	76.7401	607	2254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:45,029] [INFO] DFAST Taxonomy check result was written to GCF_009299835.1_ASM929983v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:45,030] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:45,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:45,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference/checkm_data
[2024-01-25 17:52:45,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:45,095] [INFO] Task started: CheckM
[2024-01-25 17:52:45,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009299835.1_ASM929983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009299835.1_ASM929983v1_genomic.fna/checkm_input GCF_009299835.1_ASM929983v1_genomic.fna/checkm_result
[2024-01-25 17:53:44,322] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:44,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:44,342] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:44,342] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:44,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009299835.1_ASM929983v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:44,343] [INFO] Task started: Blastn
[2024-01-25 17:53:44,343] [INFO] Running command: blastn -query GCF_009299835.1_ASM929983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c432f9-17ac-4dc3-8104-4f813ff640b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009299835.1_ASM929983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:46,237] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:46,239] [INFO] Selected 14 target genomes.
[2024-01-25 17:53:46,240] [INFO] Target genome list was writen to GCF_009299835.1_ASM929983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:46,257] [INFO] Task started: fastANI
[2024-01-25 17:53:46,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg9753847a-0f63-4695-9466-8bbe4c8f0f37/GCF_009299835.1_ASM929983v1_genomic.fna.gz --refList GCF_009299835.1_ASM929983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009299835.1_ASM929983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:03,666] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:03,675] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:03,676] [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_009299835.1	s__Microlunatus_B speluncae	100.0	2254	2254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013407955.1	s__Microlunatus_B parietis	83.9067	1580	2254	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_016907535.1	s__Microlunatus_C panaciterrae	78.6	557	2254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	78.5873	659	2254	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_013408315.1	s__Microlunatus_A terrae	78.5864	734	2254	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	78.2694	654	2254	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	78.0978	636	2254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000270245.1	s__Microlunatus phosphovorus	77.9746	516	2254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.907	505	2254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_014646195.1	s__Microlunatus_A endophyticus	77.8969	555	2254	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_009707365.1	s__Microlunatus_A sp009707365	77.8125	516	2254	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_900110855.1	s__Friedmanniella flava	77.5583	560	2254	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	77.4707	525	2254	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	76.7457	357	2254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:03,677] [INFO] GTDB search result was written to GCF_009299835.1_ASM929983v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:03,677] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:03,680] [INFO] DFAST_QC result json was written to GCF_009299835.1_ASM929983v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:03,681] [INFO] DFAST_QC completed!
[2024-01-25 17:54:03,681] [INFO] Total running time: 0h1m58s