[2024-01-25 19:56:05,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:05,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:05,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference
[2024-01-25 19:56:06,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:06,760] [INFO] Task started: Prodigal
[2024-01-25 19:56:06,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg791cb0de-3623-49d1-9940-19f0c45d455c/GCF_000423085.1_ASM42308v1_genomic.fna.gz | prodigal -d GCF_000423085.1_ASM42308v1_genomic.fna/cds.fna -a GCF_000423085.1_ASM42308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:17,095] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:17,095] [INFO] Task started: HMMsearch
[2024-01-25 19:56:17,096] [INFO] Running command: hmmsearch --tblout GCF_000423085.1_ASM42308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference/reference_markers.hmm GCF_000423085.1_ASM42308v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:17,408] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:17,409] [INFO] Found 6/6 markers.
[2024-01-25 19:56:17,456] [INFO] Query marker FASTA was written to GCF_000423085.1_ASM42308v1_genomic.fna/markers.fasta
[2024-01-25 19:56:17,456] [INFO] Task started: Blastn
[2024-01-25 19:56:17,456] [INFO] Running command: blastn -query GCF_000423085.1_ASM42308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference/reference_markers.fasta -out GCF_000423085.1_ASM42308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:18,538] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:18,540] [INFO] Selected 16 target genomes.
[2024-01-25 19:56:18,541] [INFO] Target genome list was writen to GCF_000423085.1_ASM42308v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:18,550] [INFO] Task started: fastANI
[2024-01-25 19:56:18,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg791cb0de-3623-49d1-9940-19f0c45d455c/GCF_000423085.1_ASM42308v1_genomic.fna.gz --refList GCF_000423085.1_ASM42308v1_genomic.fna/target_genomes.txt --output GCF_000423085.1_ASM42308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:31,508] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:31,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:31,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:31,519] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:56:31,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:31,519] [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=DSM 17626	GCA_000423085.1	266854	266854	type	True	100.0	1335	1338	95	conclusive
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	99.9909	1302	1338	95	conclusive
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.8388	456	1338	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	78.7374	459	1338	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.4743	299	1338	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.0781	310	1338	95	below_threshold
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	78.0729	336	1338	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.8638	363	1338	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.8507	336	1338	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.7263	330	1338	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	77.7255	325	1338	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	77.6962	234	1338	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	77.1663	371	1338	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	77.0509	229	1338	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	76.8785	278	1338	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.8203	240	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:31,521] [INFO] DFAST Taxonomy check result was written to GCF_000423085.1_ASM42308v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:31,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:31,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:31,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference/checkm_data
[2024-01-25 19:56:31,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:31,564] [INFO] Task started: CheckM
[2024-01-25 19:56:31,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423085.1_ASM42308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423085.1_ASM42308v1_genomic.fna/checkm_input GCF_000423085.1_ASM42308v1_genomic.fna/checkm_result
[2024-01-25 19:57:30,825] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:30,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:30,847] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:30,848] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:30,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423085.1_ASM42308v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:30,848] [INFO] Task started: Blastn
[2024-01-25 19:57:30,848] [INFO] Running command: blastn -query GCF_000423085.1_ASM42308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4107e359-70d6-4aa6-b9a4-b2a78931eccd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423085.1_ASM42308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:32,597] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:32,600] [INFO] Selected 18 target genomes.
[2024-01-25 19:57:32,600] [INFO] Target genome list was writen to GCF_000423085.1_ASM42308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:32,616] [INFO] Task started: fastANI
[2024-01-25 19:57:32,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg791cb0de-3623-49d1-9940-19f0c45d455c/GCF_000423085.1_ASM42308v1_genomic.fna.gz --refList GCF_000423085.1_ASM42308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423085.1_ASM42308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:47,874] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:47,885] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:47,885] [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	100.0	1335	1338	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	78.7294	460	1338	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	78.625	472	1338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCF_900092135.1	s__Raineyella antarctica	78.1036	333	1338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	78.0748	311	1338	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	77.8317	338	1338	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	77.7255	330	1338	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	77.721	323	1338	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	77.6316	342	1338	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	77.5835	297	1338	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_013693855.1	s__Micropruina sp013693855	77.5275	268	1338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839035.1	s__Enemella sp012839035	77.4952	241	1338	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	77.4119	286	1338	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	77.2613	213	1338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Avipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	77.2141	364	1338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105385.1	s__Microlunatus_A soli	77.2083	325	1338	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_013407955.1	s__Microlunatus_B parietis	77.1572	374	1338	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	75.9642	317	1338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:47,886] [INFO] GTDB search result was written to GCF_000423085.1_ASM42308v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:47,887] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:47,890] [INFO] DFAST_QC result json was written to GCF_000423085.1_ASM42308v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:47,890] [INFO] DFAST_QC completed!
[2024-01-25 19:57:47,890] [INFO] Total running time: 0h1m42s