[2024-01-24 12:06:13,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference
[2024-01-24 12:06:14,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,785] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c13d02d-949c-4052-8f82-cde5682548d1/GCF_006788875.1_ASM678887v1_genomic.fna.gz | prodigal -d GCF_006788875.1_ASM678887v1_genomic.fna/cds.fna -a GCF_006788875.1_ASM678887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,847] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,847] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,847] [INFO] Running command: hmmsearch --tblout GCF_006788875.1_ASM678887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference/reference_markers.hmm GCF_006788875.1_ASM678887v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,149] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,181] [INFO] Query marker FASTA was written to GCF_006788875.1_ASM678887v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,181] [INFO] Task started: Blastn
[2024-01-24 12:06:26,181] [INFO] Running command: blastn -query GCF_006788875.1_ASM678887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference/reference_markers.fasta -out GCF_006788875.1_ASM678887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,167] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:27,167] [INFO] Target genome list was writen to GCF_006788875.1_ASM678887v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,173] [INFO] Task started: fastANI
[2024-01-24 12:06:27,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c13d02d-949c-4052-8f82-cde5682548d1/GCF_006788875.1_ASM678887v1_genomic.fna.gz --refList GCF_006788875.1_ASM678887v1_genomic.fna/target_genomes.txt --output GCF_006788875.1_ASM678887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:37,534] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:37,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:37,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:37,547] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:37,547] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:06:37,547] [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
Microbacterium lindanitolerans	strain=DSM 22422	GCA_006788875.1	550448	550448	type	True	100.0	1116	1117	95	inconclusive
Microbacterium agarici	strain=DSM 21798	GCA_002563955.1	630514	630514	type	True	97.533	995	1117	95	inconclusive
Microbacterium fandaimingii	strain=HY82	GCA_011751745.2	2708079	2708079	type	True	81.3827	704	1117	95	below_threshold
Microbacterium chengjingii	strain=HY60	GCA_011751765.2	2769067	2769067	type	True	80.7566	664	1117	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	80.2339	533	1117	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	78.01	223	1117	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.8288	269	1117	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.7768	295	1117	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	77.656	224	1117	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.5475	53	1117	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.4311	219	1117	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.4109	221	1117	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.1221	240	1117	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	77.1213	165	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,551] [INFO] DFAST Taxonomy check result was written to GCF_006788875.1_ASM678887v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:37,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:37,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:37,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference/checkm_data
[2024-01-24 12:06:37,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:37,593] [INFO] Task started: CheckM
[2024-01-24 12:06:37,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006788875.1_ASM678887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006788875.1_ASM678887v1_genomic.fna/checkm_input GCF_006788875.1_ASM678887v1_genomic.fna/checkm_result
[2024-01-24 12:07:14,883] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:14,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:14,909] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:14,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:14,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006788875.1_ASM678887v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:14,910] [INFO] Task started: Blastn
[2024-01-24 12:07:14,910] [INFO] Running command: blastn -query GCF_006788875.1_ASM678887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc54f2805-1ea5-42bb-a669-e23ea418def5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006788875.1_ASM678887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,295] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:16,295] [INFO] Target genome list was writen to GCF_006788875.1_ASM678887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:16,318] [INFO] Task started: fastANI
[2024-01-24 12:07:16,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c13d02d-949c-4052-8f82-cde5682548d1/GCF_006788875.1_ASM678887v1_genomic.fna.gz --refList GCF_006788875.1_ASM678887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006788875.1_ASM678887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:26,399] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:26,417] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:26,417] [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_002563955.1	s__Microbacterium_A agarici	97.5358	995	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	97.53	97.53	0.93	0.93	2	conclusive
GCF_011751745.2	s__Microbacterium_A fandaimingii	81.3654	703	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	98.82	98.82	0.94	0.94	2	-
GCF_011751765.2	s__Microbacterium_A chengjingii	80.7619	663	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	98.92	98.92	0.94	0.94	2	-
GCF_900105715.1	s__Microbacterium_A humi	80.2407	532	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984125.1	s__Okibacterium sp001984125	78.2803	238	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014675.1	s__Labedella gwakjiensis	78.1048	253	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004959775.1	s__Agromyces sp004959775	77.9931	256	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248655.1	s__Microbacterium sp003248655	77.8113	202	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003716325.1	s__Cryobacterium_C tepidiphilum	77.7544	223	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	77.7205	258	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_014483895.1	s__Protaetiibacter sp014483895	77.7116	245	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355965.1	s__JAFIQW01 sp017355965	77.6063	240	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513675.1	s__Microbacterium sp001513675	77.5376	236	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752285.1	s__Mycetocola_A sp015752285	77.4491	241	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002362255.1	s__Microbacterium sp002362255	77.3292	233	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243275.1	s__Protaetiibacter sp003243275	77.3266	207	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:26,419] [INFO] GTDB search result was written to GCF_006788875.1_ASM678887v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:26,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:26,424] [INFO] DFAST_QC result json was written to GCF_006788875.1_ASM678887v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:26,424] [INFO] DFAST_QC completed!
[2024-01-24 12:07:26,425] [INFO] Total running time: 0h1m13s