[2024-01-24 12:09:05,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference
[2024-01-24 12:09:07,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:07,045] [INFO] Task started: Prodigal
[2024-01-24 12:09:07,045] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5b475c7-e35b-4fdc-af00-54774ae7cb47/GCF_016907535.1_ASM1690753v1_genomic.fna.gz | prodigal -d GCF_016907535.1_ASM1690753v1_genomic.fna/cds.fna -a GCF_016907535.1_ASM1690753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:18,929] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:18,929] [INFO] Task started: HMMsearch
[2024-01-24 12:09:18,930] [INFO] Running command: hmmsearch --tblout GCF_016907535.1_ASM1690753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference/reference_markers.hmm GCF_016907535.1_ASM1690753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:19,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:19,192] [INFO] Found 6/6 markers.
[2024-01-24 12:09:19,232] [INFO] Query marker FASTA was written to GCF_016907535.1_ASM1690753v1_genomic.fna/markers.fasta
[2024-01-24 12:09:19,232] [INFO] Task started: Blastn
[2024-01-24 12:09:19,233] [INFO] Running command: blastn -query GCF_016907535.1_ASM1690753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference/reference_markers.fasta -out GCF_016907535.1_ASM1690753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:20,326] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:20,330] [INFO] Selected 21 target genomes.
[2024-01-24 12:09:20,330] [INFO] Target genome list was writen to GCF_016907535.1_ASM1690753v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:20,337] [INFO] Task started: fastANI
[2024-01-24 12:09:20,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b475c7-e35b-4fdc-af00-54774ae7cb47/GCF_016907535.1_ASM1690753v1_genomic.fna.gz --refList GCF_016907535.1_ASM1690753v1_genomic.fna/target_genomes.txt --output GCF_016907535.1_ASM1690753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:39,900] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:39,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:39,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:39,922] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:39,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:39,922] [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 panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	100.0	1356	1356	95	conclusive
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	79.1103	543	1356	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	78.751	554	1356	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.6413	440	1356	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	78.5333	557	1356	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.5306	442	1356	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.4351	394	1356	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.3712	452	1356	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	78.361	448	1356	95	below_threshold
Microlunatus endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	78.2569	405	1356	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.1266	343	1356	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.9663	306	1356	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.4909	352	1356	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.4784	223	1356	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.441	337	1356	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	77.307	346	1356	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.3015	339	1356	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	77.1835	265	1356	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	76.9089	269	1356	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	76.2776	267	1356	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	76.1876	284	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:39,923] [INFO] DFAST Taxonomy check result was written to GCF_016907535.1_ASM1690753v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:39,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:39,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:39,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference/checkm_data
[2024-01-24 12:09:39,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:39,968] [INFO] Task started: CheckM
[2024-01-24 12:09:39,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907535.1_ASM1690753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907535.1_ASM1690753v1_genomic.fna/checkm_input GCF_016907535.1_ASM1690753v1_genomic.fna/checkm_result
[2024-01-24 12:10:23,347] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:23,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:23,367] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:23,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:23,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907535.1_ASM1690753v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:23,368] [INFO] Task started: Blastn
[2024-01-24 12:10:23,368] [INFO] Running command: blastn -query GCF_016907535.1_ASM1690753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aa18d04-b198-4627-b4e4-c0924d49ee9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907535.1_ASM1690753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:24,920] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:24,925] [INFO] Selected 16 target genomes.
[2024-01-24 12:10:24,925] [INFO] Target genome list was writen to GCF_016907535.1_ASM1690753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:24,937] [INFO] Task started: fastANI
[2024-01-24 12:10:24,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b475c7-e35b-4fdc-af00-54774ae7cb47/GCF_016907535.1_ASM1690753v1_genomic.fna.gz --refList GCF_016907535.1_ASM1690753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907535.1_ASM1690753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:38,178] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:38,196] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:38,197] [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_016907535.1	s__Microlunatus_C panaciterrae	100.0	1356	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876495.1	s__Friedmanniella capsulata	79.3062	554	1356	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	79.1266	541	1356	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_900105065.1	s__Friedmanniella luteola	79.0274	548	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805915.1	s__CADCUO01 sp902805915	78.9181	382	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__CADCUO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	78.8391	510	1356	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	78.747	554	1356	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_000270245.1	s__Microlunatus phosphovorus	78.6232	442	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299835.1	s__Microlunatus_B speluncae	78.5245	558	1356	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_016907175.1	s__Friedmanniella spumicola	78.4254	433	1356	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	78.4192	395	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_009742705.1	s__Auraticoccus cholistanensis	78.3781	445	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	78.3717	452	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707365.1	s__Microlunatus_A sp009707365	78.0592	393	1356	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_004362375.1	s__Enemella evansiae	78.0493	355	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCA_012719335.1	s__JAAYAO01 sp012719335	77.1323	176	1356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__JAAYAO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:38,199] [INFO] GTDB search result was written to GCF_016907535.1_ASM1690753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:38,200] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:38,204] [INFO] DFAST_QC result json was written to GCF_016907535.1_ASM1690753v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:38,204] [INFO] DFAST_QC completed!
[2024-01-24 12:10:38,204] [INFO] Total running time: 0h1m32s