[2024-01-25 19:35:51,309] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference
[2024-01-25 19:35:52,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,605] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cea53ed-ce2b-43bb-a579-9c371d03c349/GCF_002563955.1_ASM256395v1_genomic.fna.gz | prodigal -d GCF_002563955.1_ASM256395v1_genomic.fna/cds.fna -a GCF_002563955.1_ASM256395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:01,642] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:01,642] [INFO] Task started: HMMsearch
[2024-01-25 19:36:01,642] [INFO] Running command: hmmsearch --tblout GCF_002563955.1_ASM256395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference/reference_markers.hmm GCF_002563955.1_ASM256395v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:01,912] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:01,916] [INFO] Found 6/6 markers.
[2024-01-25 19:36:01,949] [INFO] Query marker FASTA was written to GCF_002563955.1_ASM256395v1_genomic.fna/markers.fasta
[2024-01-25 19:36:01,949] [INFO] Task started: Blastn
[2024-01-25 19:36:01,949] [INFO] Running command: blastn -query GCF_002563955.1_ASM256395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference/reference_markers.fasta -out GCF_002563955.1_ASM256395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:02,884] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:02,888] [INFO] Selected 15 target genomes.
[2024-01-25 19:36:02,888] [INFO] Target genome list was writen to GCF_002563955.1_ASM256395v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:02,898] [INFO] Task started: fastANI
[2024-01-25 19:36:02,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cea53ed-ce2b-43bb-a579-9c371d03c349/GCF_002563955.1_ASM256395v1_genomic.fna.gz --refList GCF_002563955.1_ASM256395v1_genomic.fna/target_genomes.txt --output GCF_002563955.1_ASM256395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:13,010] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:13,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:13,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:13,021] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:36:13,021] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:36:13,022] [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 agarici	strain=DSM 21798	GCA_002563955.1	630514	630514	type	True	100.0	1075	1077	95	inconclusive
Microbacterium lindanitolerans	strain=DSM 22422	GCA_006788875.1	550448	550448	type	True	97.5201	999	1077	95	inconclusive
Microbacterium fandaimingii	strain=HY82	GCA_011751745.2	2708079	2708079	type	True	81.2678	714	1077	95	below_threshold
Microbacterium chengjingii	strain=HY60	GCA_011751765.2	2769067	2769067	type	True	80.7538	678	1077	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	80.1447	554	1077	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.9889	286	1077	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	77.9415	225	1077	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	77.8456	224	1077	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.7761	288	1077	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	77.6262	229	1077	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	77.516	210	1077	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.4417	232	1077	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	77.4073	235	1077	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	77.2105	195	1077	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.3627	144	1077	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:13,023] [INFO] DFAST Taxonomy check result was written to GCF_002563955.1_ASM256395v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:13,024] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:13,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:13,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference/checkm_data
[2024-01-25 19:36:13,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:13,060] [INFO] Task started: CheckM
[2024-01-25 19:36:13,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563955.1_ASM256395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563955.1_ASM256395v1_genomic.fna/checkm_input GCF_002563955.1_ASM256395v1_genomic.fna/checkm_result
[2024-01-25 19:36:47,203] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:47,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:47,221] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:47,222] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:47,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563955.1_ASM256395v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:47,222] [INFO] Task started: Blastn
[2024-01-25 19:36:47,222] [INFO] Running command: blastn -query GCF_002563955.1_ASM256395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27b68917-c494-4967-8e75-afaba6e1d2e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563955.1_ASM256395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:48,583] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:48,587] [INFO] Selected 19 target genomes.
[2024-01-25 19:36:48,587] [INFO] Target genome list was writen to GCF_002563955.1_ASM256395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:48,609] [INFO] Task started: fastANI
[2024-01-25 19:36:48,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cea53ed-ce2b-43bb-a579-9c371d03c349/GCF_002563955.1_ASM256395v1_genomic.fna.gz --refList GCF_002563955.1_ASM256395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563955.1_ASM256395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:00,512] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:00,525] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:00,525] [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	100.0	1075	1077	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	81.2521	716	1077	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	80.7538	678	1077	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	80.1545	553	1077	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_900115155.1	s__Mycetocola_A miduiensis	78.009	222	1077	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_003627075.1	s__Protaetiibacter intestinalis	77.9415	225	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	77.936	266	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	77.9109	277	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078635.1	s__Labedella phragmitis	77.9103	288	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	77.8183	244	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752285.1	s__Mycetocola_A sp015752285	77.7124	215	1077	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_003990045.1	s__Labedella endophytica	77.6783	267	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513675.1	s__Microbacterium sp001513675	77.6329	231	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	77.5949	240	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010686705.1	s__Diaminobutyricibacter tongyongensis	77.5874	226	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355965.1	s__JAFIQW01 sp017355965	77.5314	260	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	77.4744	188	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCF_002362255.1	s__Microbacterium sp002362255	77.425	227	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999995.1	s__Microbacterium sp003999995	77.4199	234	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:00,527] [INFO] GTDB search result was written to GCF_002563955.1_ASM256395v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:00,528] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:00,532] [INFO] DFAST_QC result json was written to GCF_002563955.1_ASM256395v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:00,532] [INFO] DFAST_QC completed!
[2024-01-25 19:37:00,532] [INFO] Total running time: 0h1m9s