[2024-01-24 13:25:45,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:45,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:45,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference
[2024-01-24 13:25:47,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:47,178] [INFO] Task started: Prodigal
[2024-01-24 13:25:47,178] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9f448d5-ac49-4b2f-88a8-6d4302e7d989/GCF_011047135.1_ASM1104713v1_genomic.fna.gz | prodigal -d GCF_011047135.1_ASM1104713v1_genomic.fna/cds.fna -a GCF_011047135.1_ASM1104713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:57,770] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:57,771] [INFO] Task started: HMMsearch
[2024-01-24 13:25:57,771] [INFO] Running command: hmmsearch --tblout GCF_011047135.1_ASM1104713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference/reference_markers.hmm GCF_011047135.1_ASM1104713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:58,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:58,022] [INFO] Found 6/6 markers.
[2024-01-24 13:25:58,058] [INFO] Query marker FASTA was written to GCF_011047135.1_ASM1104713v1_genomic.fna/markers.fasta
[2024-01-24 13:25:58,059] [INFO] Task started: Blastn
[2024-01-24 13:25:58,059] [INFO] Running command: blastn -query GCF_011047135.1_ASM1104713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference/reference_markers.fasta -out GCF_011047135.1_ASM1104713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:58,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:58,921] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:58,922] [INFO] Target genome list was writen to GCF_011047135.1_ASM1104713v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:58,927] [INFO] Task started: fastANI
[2024-01-24 13:25:58,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f448d5-ac49-4b2f-88a8-6d4302e7d989/GCF_011047135.1_ASM1104713v1_genomic.fna.gz --refList GCF_011047135.1_ASM1104713v1_genomic.fna/target_genomes.txt --output GCF_011047135.1_ASM1104713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:07,235] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:07,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:07,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:07,246] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:26:07,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:07,246] [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 endophyticum	strain=DSM 27099	GCA_011047135.1	1526412	1526412	type	True	100.0	971	972	95	conclusive
Microbacterium endophyticum	strain=DSM 27099	GCA_014191465.1	1526412	1526412	type	True	99.9965	947	972	95	conclusive
Microbacterium endophyticum	strain=CECT 8354	GCA_011761445.1	1526412	1526412	type	True	99.9959	965	972	95	conclusive
Microbacterium halimionae	strain=CECT 8593	GCA_011761265.1	1526413	1526413	type	True	85.7283	726	972	95	below_threshold
Microbacterium halimionae	strain=DSM 27576	GCA_014137985.1	1526413	1526413	type	True	85.7157	726	972	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	77.9837	222	972	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	77.9799	222	972	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.3225	142	972	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.2584	136	972	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	77.0454	101	972	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	76.5999	54	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:07,248] [INFO] DFAST Taxonomy check result was written to GCF_011047135.1_ASM1104713v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:07,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:07,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:07,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference/checkm_data
[2024-01-24 13:26:07,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:07,282] [INFO] Task started: CheckM
[2024-01-24 13:26:07,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011047135.1_ASM1104713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011047135.1_ASM1104713v1_genomic.fna/checkm_input GCF_011047135.1_ASM1104713v1_genomic.fna/checkm_result
[2024-01-24 13:26:41,326] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:41,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:41,345] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:41,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:41,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011047135.1_ASM1104713v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:41,346] [INFO] Task started: Blastn
[2024-01-24 13:26:41,347] [INFO] Running command: blastn -query GCF_011047135.1_ASM1104713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04306838-00b3-4102-ae60-90bcd07fb4a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_011047135.1_ASM1104713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:42,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:42,613] [INFO] Selected 22 target genomes.
[2024-01-24 13:26:42,613] [INFO] Target genome list was writen to GCF_011047135.1_ASM1104713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:42,629] [INFO] Task started: fastANI
[2024-01-24 13:26:42,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f448d5-ac49-4b2f-88a8-6d4302e7d989/GCF_011047135.1_ASM1104713v1_genomic.fna.gz --refList GCF_011047135.1_ASM1104713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011047135.1_ASM1104713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:55,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:55,200] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:55,201] [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_011047135.1	s__Microbacterium endophyticum	100.0	972	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	0.99	3	conclusive
GCF_011761265.1	s__Microbacterium halimionae	85.7283	726	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006783905.1	s__Microbacterium kyungheense	78.4259	235	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	78.2917	237	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201255.1	s__Microbacterium sp014201255	78.2761	204	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	78.1492	229	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427525.1	s__Microbacterium sp001427525	78.1253	243	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635115.1	s__Microbacterium sp003635115	78.125	244	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	78.0402	230	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	78.0286	264	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716815.1	s__Microbacterium lacticum	78.025	223	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCF_007828185.1	s__Microbacterium sp007828185	78.0199	231	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292075.1	s__Microbacterium timonense	78.0084	221	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339645.1	s__Microbacterium arborescens	78.0012	233	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_014779795.1	s__Microbacterium helvum	77.975	259	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564355.1	s__Microbacterium wangchenii	77.9558	226	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.29	98.90	0.96	0.95	3	-
GCF_012847295.1	s__Microbacterium sp012847295	77.9549	225	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003991875.1	s__Microbacterium lemovicicum	77.8984	242	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314225.1	s__Microbacterium sp001314225	77.8576	224	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014197265.1	s__Microbacterium invictum	77.8528	221	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017968845.1	s__Microbacterium sp017968845	77.8058	160	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710705.1	s__Microbacterium radiodurans	77.6398	234	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:55,202] [INFO] GTDB search result was written to GCF_011047135.1_ASM1104713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:55,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:55,206] [INFO] DFAST_QC result json was written to GCF_011047135.1_ASM1104713v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:55,207] [INFO] DFAST_QC completed!
[2024-01-24 13:26:55,207] [INFO] Total running time: 0h1m9s