[2023-06-29 14:21:47,352] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:21:47,354] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:21:47,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference
[2023-06-29 14:21:48,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:21:48,755] [INFO] Task started: Prodigal
[2023-06-29 14:21:48,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eb481a9-e43b-4827-a970-d14e42760c19/GCA_011620705.1_ASM1162070v1_genomic.fna.gz | prodigal -d GCA_011620705.1_ASM1162070v1_genomic.fna/cds.fna -a GCA_011620705.1_ASM1162070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:21:53,871] [INFO] Task succeeded: Prodigal
[2023-06-29 14:21:53,872] [INFO] Task started: HMMsearch
[2023-06-29 14:21:53,872] [INFO] Running command: hmmsearch --tblout GCA_011620705.1_ASM1162070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference/reference_markers.hmm GCA_011620705.1_ASM1162070v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:21:54,205] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:21:54,207] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2eb481a9-e43b-4827-a970-d14e42760c19/GCA_011620705.1_ASM1162070v1_genomic.fna.gz]
[2023-06-29 14:21:54,234] [INFO] Query marker FASTA was written to GCA_011620705.1_ASM1162070v1_genomic.fna/markers.fasta
[2023-06-29 14:21:54,235] [INFO] Task started: Blastn
[2023-06-29 14:21:54,235] [INFO] Running command: blastn -query GCA_011620705.1_ASM1162070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference/reference_markers.fasta -out GCA_011620705.1_ASM1162070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:21:55,362] [INFO] Task succeeded: Blastn
[2023-06-29 14:21:55,366] [INFO] Selected 23 target genomes.
[2023-06-29 14:21:55,366] [INFO] Target genome list was writen to GCA_011620705.1_ASM1162070v1_genomic.fna/target_genomes.txt
[2023-06-29 14:21:55,368] [INFO] Task started: fastANI
[2023-06-29 14:21:55,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb481a9-e43b-4827-a970-d14e42760c19/GCA_011620705.1_ASM1162070v1_genomic.fna.gz --refList GCA_011620705.1_ASM1162070v1_genomic.fna/target_genomes.txt --output GCA_011620705.1_ASM1162070v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:22:08,747] [INFO] Task succeeded: fastANI
[2023-06-29 14:22:08,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:22:08,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:22:08,766] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:22:08,766] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:22:08,767] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.7656	318	563	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.6667	305	563	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	78.5159	177	563	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.5041	245	563	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.5001	245	563	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	78.4988	185	563	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.48	232	563	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	78.4563	265	563	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.2827	214	563	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.226	250	563	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	78.1733	214	563	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.1198	219	563	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.1027	237	563	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.0969	219	563	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.0873	225	563	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.077	211	563	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	77.9177	240	563	95	below_threshold
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	77.8387	215	563	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	77.8283	176	563	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	77.7667	166	563	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	77.5794	204	563	95	below_threshold
Microbacterium luteum	strain=A18JL200	GCA_015277875.1	2782167	2782167	type	True	77.4936	159	563	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	77.1943	146	563	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:22:08,769] [INFO] DFAST Taxonomy check result was written to GCA_011620705.1_ASM1162070v1_genomic.fna/tc_result.tsv
[2023-06-29 14:22:08,770] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:22:08,770] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:22:08,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference/checkm_data
[2023-06-29 14:22:08,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:22:08,800] [INFO] Task started: CheckM
[2023-06-29 14:22:08,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011620705.1_ASM1162070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011620705.1_ASM1162070v1_genomic.fna/checkm_input GCA_011620705.1_ASM1162070v1_genomic.fna/checkm_result
[2023-06-29 14:22:29,598] [INFO] Task succeeded: CheckM
[2023-06-29 14:22:29,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:22:29,622] [INFO] ===== Completeness check finished =====
[2023-06-29 14:22:29,622] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:22:29,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011620705.1_ASM1162070v1_genomic.fna/markers.fasta)
[2023-06-29 14:22:29,623] [INFO] Task started: Blastn
[2023-06-29 14:22:29,623] [INFO] Running command: blastn -query GCA_011620705.1_ASM1162070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg988ad208-787d-42e0-abfd-accb6bfb6827/dqc_reference/reference_markers_gtdb.fasta -out GCA_011620705.1_ASM1162070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:22:31,155] [INFO] Task succeeded: Blastn
[2023-06-29 14:22:31,160] [INFO] Selected 16 target genomes.
[2023-06-29 14:22:31,160] [INFO] Target genome list was writen to GCA_011620705.1_ASM1162070v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:22:31,163] [INFO] Task started: fastANI
[2023-06-29 14:22:31,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb481a9-e43b-4827-a970-d14e42760c19/GCA_011620705.1_ASM1162070v1_genomic.fna.gz --refList GCA_011620705.1_ASM1162070v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011620705.1_ASM1162070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:22:39,846] [INFO] Task succeeded: fastANI
[2023-06-29 14:22:39,860] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:22:39,860] [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
GCA_011620705.1	s__Pseudolysinimonas sp011620705	100.0	550	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003243275.1	s__Protaetiibacter sp003243275	79.8258	290	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.7559	319	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216815.1	s__Protaetiibacter sp004216815	79.6938	301	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517535.1	s__Schumannella sp006517535	79.6408	306	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	79.5565	279	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCA_017308515.1	s__Pseudolysinimonas sp017308515	79.4263	296	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517435.1	s__Schumannella sp006517435	79.4035	312	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	79.396	286	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	79.351	312	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014653215.1	s__Pseudolysinimonas yzui	79.3298	313	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012530535.1	s__Yonghaparkia sp012530535	78.9257	256	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479755.1	s__Pseudolysinimonas sp905479755	78.8396	263	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017545.1	s__Protaetiibacter sp008017545	78.5302	254	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627055.1	s__Gryllotalpicola protaetiae	78.2058	212	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581425.1	s__Amnibacterium setariae	77.8228	216	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:22:39,862] [INFO] GTDB search result was written to GCA_011620705.1_ASM1162070v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:22:39,863] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:22:39,870] [INFO] DFAST_QC result json was written to GCA_011620705.1_ASM1162070v1_genomic.fna/dqc_result.json
[2023-06-29 14:22:39,871] [INFO] DFAST_QC completed!
[2023-06-29 14:22:39,871] [INFO] Total running time: 0h0m53s