[2024-01-24 13:40:46,052] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference
[2024-01-24 13:40:47,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,356] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg1302cb51-94f2-4c17-861d-8e6dc933f5ac/GCF_014137855.1_ASM1413785v1_genomic.fna.gz | prodigal -d GCF_014137855.1_ASM1413785v1_genomic.fna/cds.fna -a GCF_014137855.1_ASM1413785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,467] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,468] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,468] [INFO] Running command: hmmsearch --tblout GCF_014137855.1_ASM1413785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference/reference_markers.hmm GCF_014137855.1_ASM1413785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,743] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,791] [INFO] Query marker FASTA was written to GCF_014137855.1_ASM1413785v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,791] [INFO] Task started: Blastn
[2024-01-24 13:40:58,791] [INFO] Running command: blastn -query GCF_014137855.1_ASM1413785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference/reference_markers.fasta -out GCF_014137855.1_ASM1413785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,978] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:59,978] [INFO] Target genome list was writen to GCF_014137855.1_ASM1413785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,142] [INFO] Task started: fastANI
[2024-01-24 13:41:00,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg1302cb51-94f2-4c17-861d-8e6dc933f5ac/GCF_014137855.1_ASM1413785v1_genomic.fna.gz --refList GCF_014137855.1_ASM1413785v1_genomic.fna/target_genomes.txt --output GCF_014137855.1_ASM1413785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:18,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:18,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:18,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:18,213] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:18,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:18,214] [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 kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	100.0	1429	1431	95	conclusive
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	79.3326	660	1431	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	79.2164	684	1431	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	79.1188	533	1431	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	79.1133	589	1431	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	79.0351	558	1431	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	79.0166	608	1431	95	below_threshold
Microlunatus endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	78.7275	544	1431	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.7138	482	1431	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	78.6791	674	1431	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	78.5955	644	1431	95	below_threshold
Microlunatus soli	strain=DSM 21800	GCA_900105385.1	630515	630515	type	True	78.5335	611	1431	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.5306	603	1431	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	77.5887	329	1431	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	77.4001	468	1431	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.3824	491	1431	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.205	415	1431	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	76.891	460	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:18,215] [INFO] DFAST Taxonomy check result was written to GCF_014137855.1_ASM1413785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:18,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:18,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:18,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference/checkm_data
[2024-01-24 13:41:18,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:18,262] [INFO] Task started: CheckM
[2024-01-24 13:41:18,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137855.1_ASM1413785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137855.1_ASM1413785v1_genomic.fna/checkm_input GCF_014137855.1_ASM1413785v1_genomic.fna/checkm_result
[2024-01-24 13:42:16,474] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:16,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,497] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:16,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:16,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137855.1_ASM1413785v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:16,499] [INFO] Task started: Blastn
[2024-01-24 13:42:16,499] [INFO] Running command: blastn -query GCF_014137855.1_ASM1413785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg307ee265-97ea-49f9-aa0c-1e086c9b3fb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137855.1_ASM1413785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:18,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:18,322] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:18,322] [INFO] Target genome list was writen to GCF_014137855.1_ASM1413785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:18,406] [INFO] Task started: fastANI
[2024-01-24 13:42:18,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg1302cb51-94f2-4c17-861d-8e6dc933f5ac/GCF_014137855.1_ASM1413785v1_genomic.fna.gz --refList GCF_014137855.1_ASM1413785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137855.1_ASM1413785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:33,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:33,033] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:33,034] [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_014137855.1	s__Friedmanniella_A endophytica	100.0	1428	1431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876495.1	s__Friedmanniella capsulata	79.7337	743	1431	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	79.4775	706	1431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	79.441	663	1431	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_900105785.1	s__Friedmanniella sagamiharensis	79.287	667	1431	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	79.2094	685	1431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	79.107	534	1431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_016907535.1	s__Microlunatus_C panaciterrae	79.0555	557	1431	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_014646195.1	s__Microlunatus_A endophyticus	78.7267	544	1431	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_000270245.1	s__Microlunatus phosphovorus	78.6728	487	1431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407955.1	s__Microlunatus_B parietis	78.6303	682	1431	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_009299835.1	s__Microlunatus_B speluncae	78.6174	640	1431	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_900105385.1	s__Microlunatus_A soli	78.5121	615	1431	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_900101785.1	s__Auraticoccus monumenti	78.4968	608	1431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:33,035] [INFO] GTDB search result was written to GCF_014137855.1_ASM1413785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:33,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:33,039] [INFO] DFAST_QC result json was written to GCF_014137855.1_ASM1413785v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:33,039] [INFO] DFAST_QC completed!
[2024-01-24 13:42:33,040] [INFO] Total running time: 0h1m47s