[2024-01-25 19:34:21,309] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference
[2024-01-25 19:34:22,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,430] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d94eb6e-1b66-4875-857c-bd8e6606458c/GCF_014643695.1_ASM1464369v1_genomic.fna.gz | prodigal -d GCF_014643695.1_ASM1464369v1_genomic.fna/cds.fna -a GCF_014643695.1_ASM1464369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:30,666] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:30,666] [INFO] Task started: HMMsearch
[2024-01-25 19:34:30,666] [INFO] Running command: hmmsearch --tblout GCF_014643695.1_ASM1464369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference/reference_markers.hmm GCF_014643695.1_ASM1464369v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:30,877] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:30,878] [INFO] Found 6/6 markers.
[2024-01-25 19:34:30,907] [INFO] Query marker FASTA was written to GCF_014643695.1_ASM1464369v1_genomic.fna/markers.fasta
[2024-01-25 19:34:30,907] [INFO] Task started: Blastn
[2024-01-25 19:34:30,907] [INFO] Running command: blastn -query GCF_014643695.1_ASM1464369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference/reference_markers.fasta -out GCF_014643695.1_ASM1464369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:32,096] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:32,099] [INFO] Selected 14 target genomes.
[2024-01-25 19:34:32,099] [INFO] Target genome list was writen to GCF_014643695.1_ASM1464369v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:32,103] [INFO] Task started: fastANI
[2024-01-25 19:34:32,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d94eb6e-1b66-4875-857c-bd8e6606458c/GCF_014643695.1_ASM1464369v1_genomic.fna.gz --refList GCF_014643695.1_ASM1464369v1_genomic.fna/target_genomes.txt --output GCF_014643695.1_ASM1464369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:42,112] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:42,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:42,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:42,122] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:34:42,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:42,122] [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 album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	100.0	1110	1112	95	conclusive
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	82.1116	614	1112	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	81.4603	508	1112	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	81.3214	520	1112	95	below_threshold
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	81.1505	543	1112	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.6775	488	1112	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	79.9743	452	1112	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8688	430	1112	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	79.8355	424	1112	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	79.8309	452	1112	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.6894	399	1112	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.5911	409	1112	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.489	425	1112	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	79.4582	437	1112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:42,123] [INFO] DFAST Taxonomy check result was written to GCF_014643695.1_ASM1464369v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:42,124] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:42,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:42,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference/checkm_data
[2024-01-25 19:34:42,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:42,159] [INFO] Task started: CheckM
[2024-01-25 19:34:42,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643695.1_ASM1464369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643695.1_ASM1464369v1_genomic.fna/checkm_input GCF_014643695.1_ASM1464369v1_genomic.fna/checkm_result
[2024-01-25 19:35:15,866] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:15,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:15,888] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:15,888] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:15,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643695.1_ASM1464369v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:15,889] [INFO] Task started: Blastn
[2024-01-25 19:35:15,889] [INFO] Running command: blastn -query GCF_014643695.1_ASM1464369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7130e9e8-33d5-40c9-8d54-63385789cc94/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643695.1_ASM1464369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:17,831] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:17,834] [INFO] Selected 8 target genomes.
[2024-01-25 19:35:17,835] [INFO] Target genome list was writen to GCF_014643695.1_ASM1464369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:17,839] [INFO] Task started: fastANI
[2024-01-25 19:35:17,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d94eb6e-1b66-4875-857c-bd8e6606458c/GCF_014643695.1_ASM1464369v1_genomic.fna.gz --refList GCF_014643695.1_ASM1464369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643695.1_ASM1464369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:23,792] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:23,798] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:23,798] [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_014643695.1	s__Microbacterium album	100.0	1110	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001426925.1	s__Microbacterium sp001426925	83.1216	577	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_016805985.1	s__Microbacterium sp016805985	82.6099	601	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015235415.1	s__Microbacterium paludicola_A	82.4976	562	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004564075.1	s__Microbacterium sediminis	81.4243	511	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_017592545.1	s__Microbacterium sp017592545	81.2228	538	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735645.1	s__Microbacterium oryzae	80.7024	486	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970975.1	s__Microbacterium halophytorum	79.819	453	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:23,800] [INFO] GTDB search result was written to GCF_014643695.1_ASM1464369v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:23,801] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:23,805] [INFO] DFAST_QC result json was written to GCF_014643695.1_ASM1464369v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:23,805] [INFO] DFAST_QC completed!
[2024-01-25 19:35:23,805] [INFO] Total running time: 0h1m2s