[2024-01-25 17:35:35,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference
[2024-01-25 17:35:36,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,668] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,669] [INFO] Running command: gunzip -c /var/lib/cwl/stga624565f-2341-47ec-a0ec-01588e9d4d94/GCF_014836945.1_ASM1483694v1_genomic.fna.gz | prodigal -d GCF_014836945.1_ASM1483694v1_genomic.fna/cds.fna -a GCF_014836945.1_ASM1483694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:43,803] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:43,804] [INFO] Task started: HMMsearch
[2024-01-25 17:35:43,804] [INFO] Running command: hmmsearch --tblout GCF_014836945.1_ASM1483694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference/reference_markers.hmm GCF_014836945.1_ASM1483694v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:44,014] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:44,015] [INFO] Found 6/6 markers.
[2024-01-25 17:35:44,040] [INFO] Query marker FASTA was written to GCF_014836945.1_ASM1483694v1_genomic.fna/markers.fasta
[2024-01-25 17:35:44,040] [INFO] Task started: Blastn
[2024-01-25 17:35:44,040] [INFO] Running command: blastn -query GCF_014836945.1_ASM1483694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference/reference_markers.fasta -out GCF_014836945.1_ASM1483694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:45,281] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:45,284] [INFO] Selected 17 target genomes.
[2024-01-25 17:35:45,284] [INFO] Target genome list was writen to GCF_014836945.1_ASM1483694v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:45,287] [INFO] Task started: fastANI
[2024-01-25 17:35:45,287] [INFO] Running command: fastANI --query /var/lib/cwl/stga624565f-2341-47ec-a0ec-01588e9d4d94/GCF_014836945.1_ASM1483694v1_genomic.fna.gz --refList GCF_014836945.1_ASM1483694v1_genomic.fna/target_genomes.txt --output GCF_014836945.1_ASM1483694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:57,070] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:57,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:57,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:57,081] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:57,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:57,081] [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 commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	100.0	908	909	95	conclusive
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	86.1941	728	909	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	82.3932	630	909	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	81.6363	558	909	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	81.5918	566	909	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	81.4717	520	909	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	81.4703	573	909	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	81.3604	523	909	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	81.329	534	909	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	81.273	573	909	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	81.1417	547	909	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	80.8225	497	909	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	80.1979	417	909	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.1833	477	909	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	80.1573	421	909	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.1545	453	909	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.6729	467	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:57,082] [INFO] DFAST Taxonomy check result was written to GCF_014836945.1_ASM1483694v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:57,083] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:57,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:57,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference/checkm_data
[2024-01-25 17:35:57,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:57,114] [INFO] Task started: CheckM
[2024-01-25 17:35:57,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836945.1_ASM1483694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836945.1_ASM1483694v1_genomic.fna/checkm_input GCF_014836945.1_ASM1483694v1_genomic.fna/checkm_result
[2024-01-25 17:36:40,534] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:40,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:40,559] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:40,560] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:40,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836945.1_ASM1483694v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:40,561] [INFO] Task started: Blastn
[2024-01-25 17:36:40,561] [INFO] Running command: blastn -query GCF_014836945.1_ASM1483694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37219bce-2a67-4f64-870d-f77e4de60992/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836945.1_ASM1483694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:42,564] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:42,567] [INFO] Selected 6 target genomes.
[2024-01-25 17:36:42,567] [INFO] Target genome list was writen to GCF_014836945.1_ASM1483694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:42,572] [INFO] Task started: fastANI
[2024-01-25 17:36:42,572] [INFO] Running command: fastANI --query /var/lib/cwl/stga624565f-2341-47ec-a0ec-01588e9d4d94/GCF_014836945.1_ASM1483694v1_genomic.fna.gz --refList GCF_014836945.1_ASM1483694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836945.1_ASM1483694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:47,590] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:47,595] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:47,596] [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_001878835.1	s__Microbacterium sp001878835	98.5562	789	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.56	98.56	0.87	0.87	2	conclusive
GCA_002837415.1	s__Microbacterium sp002837415	89.4838	724	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	88.0224	759	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_014084045.1	s__Microbacterium esteraromaticum_D	86.4238	725	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907315.1	s__Microbacterium esteraromaticum	86.1789	727	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015040615.1	s__Microbacterium sp015040615	84.0533	679	909	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 17:36:47,597] [INFO] GTDB search result was written to GCF_014836945.1_ASM1483694v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:47,598] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:47,601] [INFO] DFAST_QC result json was written to GCF_014836945.1_ASM1483694v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:47,601] [INFO] DFAST_QC completed!
[2024-01-25 17:36:47,601] [INFO] Total running time: 0h1m12s