[2024-01-24 12:44:54,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:54,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:54,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference
[2024-01-24 12:44:55,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,720] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ab57e8c-dd33-46aa-871a-d42d4369fce2/GCF_027921765.1_ASM2792176v1_genomic.fna.gz | prodigal -d GCF_027921765.1_ASM2792176v1_genomic.fna/cds.fna -a GCF_027921765.1_ASM2792176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:05,431] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:05,432] [INFO] Task started: HMMsearch
[2024-01-24 12:45:05,432] [INFO] Running command: hmmsearch --tblout GCF_027921765.1_ASM2792176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference/reference_markers.hmm GCF_027921765.1_ASM2792176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:05,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:05,720] [INFO] Found 6/6 markers.
[2024-01-24 12:45:05,754] [INFO] Query marker FASTA was written to GCF_027921765.1_ASM2792176v1_genomic.fna/markers.fasta
[2024-01-24 12:45:05,754] [INFO] Task started: Blastn
[2024-01-24 12:45:05,754] [INFO] Running command: blastn -query GCF_027921765.1_ASM2792176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference/reference_markers.fasta -out GCF_027921765.1_ASM2792176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:07,098] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:07,101] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:07,102] [INFO] Target genome list was writen to GCF_027921765.1_ASM2792176v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:07,106] [INFO] Task started: fastANI
[2024-01-24 12:45:07,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab57e8c-dd33-46aa-871a-d42d4369fce2/GCF_027921765.1_ASM2792176v1_genomic.fna.gz --refList GCF_027921765.1_ASM2792176v1_genomic.fna/target_genomes.txt --output GCF_027921765.1_ASM2792176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:17,506] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:17,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:17,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:17,525] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:17,525] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:17,526] [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 oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	84.9999	745	1146	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	81.6486	538	1146	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	81.6313	539	1146	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	81.5407	542	1146	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	81.0133	520	1146	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	80.9605	574	1146	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	80.6311	535	1146	95	below_threshold
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	80.532	585	1146	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	80.2321	555	1146	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.1482	501	1146	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.0482	455	1146	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.9621	509	1146	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	79.953	531	1146	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.5926	510	1146	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0944	492	1146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:17,528] [INFO] DFAST Taxonomy check result was written to GCF_027921765.1_ASM2792176v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:17,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:17,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:17,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference/checkm_data
[2024-01-24 12:45:17,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:17,568] [INFO] Task started: CheckM
[2024-01-24 12:45:17,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921765.1_ASM2792176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921765.1_ASM2792176v1_genomic.fna/checkm_input GCF_027921765.1_ASM2792176v1_genomic.fna/checkm_result
[2024-01-24 12:46:04,524] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:04,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:04,550] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:04,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:04,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921765.1_ASM2792176v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:04,551] [INFO] Task started: Blastn
[2024-01-24 12:46:04,551] [INFO] Running command: blastn -query GCF_027921765.1_ASM2792176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg183accad-4624-420f-b25b-755dae5275f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921765.1_ASM2792176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:06,950] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:06,955] [INFO] Selected 12 target genomes.
[2024-01-24 12:46:06,955] [INFO] Target genome list was writen to GCF_027921765.1_ASM2792176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:06,974] [INFO] Task started: fastANI
[2024-01-24 12:46:06,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab57e8c-dd33-46aa-871a-d42d4369fce2/GCF_027921765.1_ASM2792176v1_genomic.fna.gz --refList GCF_027921765.1_ASM2792176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921765.1_ASM2792176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:16,444] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:16,457] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:16,457] [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_009735645.1	s__Microbacterium oryzae	85.0141	744	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426925.1	s__Microbacterium sp001426925	82.0362	590	1146	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	81.6057	605	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564075.1	s__Microbacterium sediminis	81.5306	543	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_015235415.1	s__Microbacterium paludicola_A	81.5165	587	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014643695.1	s__Microbacterium album	81.0081	521	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592545.1	s__Microbacterium sp017592545	80.5696	583	1146	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	80.1948	558	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018588945.1	s__Microbacterium flavescens	80.1244	503	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759705.1	s__Microbacterium ulmi	79.9535	531	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902706225.1	s__Microbacterium sp902706225	79.6758	489	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306415.1	s__Microbacterium sp001897105	79.458	460	1146	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.03	95.75	0.95	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:16,459] [INFO] GTDB search result was written to GCF_027921765.1_ASM2792176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:16,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:16,463] [INFO] DFAST_QC result json was written to GCF_027921765.1_ASM2792176v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:16,463] [INFO] DFAST_QC completed!
[2024-01-24 12:46:16,463] [INFO] Total running time: 0h1m22s