[2024-01-25 17:58:50,783] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference
[2024-01-25 17:58:52,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:52,017] [INFO] Task started: Prodigal
[2024-01-25 17:58:52,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ab6a729-d271-4ff3-9478-d8c3e9482775/GCF_028737415.2_ASM2873741v2_genomic.fna.gz | prodigal -d GCF_028737415.2_ASM2873741v2_genomic.fna/cds.fna -a GCF_028737415.2_ASM2873741v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:58,836] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:58,836] [INFO] Task started: HMMsearch
[2024-01-25 17:58:58,836] [INFO] Running command: hmmsearch --tblout GCF_028737415.2_ASM2873741v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference/reference_markers.hmm GCF_028737415.2_ASM2873741v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:59,028] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:59,029] [INFO] Found 6/6 markers.
[2024-01-25 17:58:59,058] [INFO] Query marker FASTA was written to GCF_028737415.2_ASM2873741v2_genomic.fna/markers.fasta
[2024-01-25 17:58:59,058] [INFO] Task started: Blastn
[2024-01-25 17:58:59,058] [INFO] Running command: blastn -query GCF_028737415.2_ASM2873741v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference/reference_markers.fasta -out GCF_028737415.2_ASM2873741v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:00,185] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:00,189] [INFO] Selected 17 target genomes.
[2024-01-25 17:59:00,189] [INFO] Target genome list was writen to GCF_028737415.2_ASM2873741v2_genomic.fna/target_genomes.txt
[2024-01-25 17:59:00,202] [INFO] Task started: fastANI
[2024-01-25 17:59:00,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab6a729-d271-4ff3-9478-d8c3e9482775/GCF_028737415.2_ASM2873741v2_genomic.fna.gz --refList GCF_028737415.2_ASM2873741v2_genomic.fna/target_genomes.txt --output GCF_028737415.2_ASM2873741v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:11,962] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:11,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:11,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:11,972] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:11,973] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:11,973] [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 imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	91.3415	848	920	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	84.2095	710	920	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	81.6243	502	920	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.5655	532	920	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	81.5507	536	920	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	81.4756	541	920	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.385	538	920	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.2065	553	920	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.0813	523	920	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.9629	499	920	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.8692	510	920	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.8312	520	920	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.7436	547	920	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.6127	484	920	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.5785	509	920	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.5273	489	920	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.2985	526	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:11,974] [INFO] DFAST Taxonomy check result was written to GCF_028737415.2_ASM2873741v2_genomic.fna/tc_result.tsv
[2024-01-25 17:59:11,975] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:11,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:11,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference/checkm_data
[2024-01-25 17:59:11,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:12,006] [INFO] Task started: CheckM
[2024-01-25 17:59:12,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028737415.2_ASM2873741v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028737415.2_ASM2873741v2_genomic.fna/checkm_input GCF_028737415.2_ASM2873741v2_genomic.fna/checkm_result
[2024-01-25 17:59:39,733] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:39,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:39,757] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:39,757] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:39,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028737415.2_ASM2873741v2_genomic.fna/markers.fasta)
[2024-01-25 17:59:39,760] [INFO] Task started: Blastn
[2024-01-25 17:59:39,760] [INFO] Running command: blastn -query GCF_028737415.2_ASM2873741v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg339a6848-4dac-4117-bbe7-d1dd2445c269/dqc_reference/reference_markers_gtdb.fasta -out GCF_028737415.2_ASM2873741v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:41,698] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:41,701] [INFO] Selected 7 target genomes.
[2024-01-25 17:59:41,701] [INFO] Target genome list was writen to GCF_028737415.2_ASM2873741v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:41,709] [INFO] Task started: fastANI
[2024-01-25 17:59:41,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab6a729-d271-4ff3-9478-d8c3e9482775/GCF_028737415.2_ASM2873741v2_genomic.fna.gz --refList GCF_028737415.2_ASM2873741v2_genomic.fna/target_genomes_gtdb.txt --output GCF_028737415.2_ASM2873741v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:47,505] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:47,511] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:59:47,511] [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_017876655.1	s__Microbacterium imperiale	91.3415	848	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245215.1	s__Microbacterium sp002245215	85.5462	789	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289625.1	s__Microbacterium sp003289625	85.454	777	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	-
GCF_003339645.1	s__Microbacterium arborescens	85.43	751	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_900102175.1	s__Microbacterium sp900102175	85.3116	719	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610405.1	s__Microbacterium sp003610405	85.2699	750	920	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013389665.1	s__Microbacterium oleivorans_C	85.1257	752	920	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 17:59:47,513] [INFO] GTDB search result was written to GCF_028737415.2_ASM2873741v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:47,513] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:47,519] [INFO] DFAST_QC result json was written to GCF_028737415.2_ASM2873741v2_genomic.fna/dqc_result.json
[2024-01-25 17:59:47,519] [INFO] DFAST_QC completed!
[2024-01-25 17:59:47,519] [INFO] Total running time: 0h0m57s