[2024-01-24 11:26:54,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,327] [INFO] DQC Reference Directory: /var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference
[2024-01-24 11:26:58,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,221] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cbe5675-bcca-4766-9cb2-dd5c021950d3/GCF_011761445.1_ASM1176144v1_genomic.fna.gz | prodigal -d GCF_011761445.1_ASM1176144v1_genomic.fna/cds.fna -a GCF_011761445.1_ASM1176144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,098] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,098] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,098] [INFO] Running command: hmmsearch --tblout GCF_011761445.1_ASM1176144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference/reference_markers.hmm GCF_011761445.1_ASM1176144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:08,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:08,356] [INFO] Found 6/6 markers.
[2024-01-24 11:27:08,383] [INFO] Query marker FASTA was written to GCF_011761445.1_ASM1176144v1_genomic.fna/markers.fasta
[2024-01-24 11:27:08,384] [INFO] Task started: Blastn
[2024-01-24 11:27:08,384] [INFO] Running command: blastn -query GCF_011761445.1_ASM1176144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference/reference_markers.fasta -out GCF_011761445.1_ASM1176144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,246] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,250] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:09,251] [INFO] Target genome list was writen to GCF_011761445.1_ASM1176144v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:09,294] [INFO] Task started: fastANI
[2024-01-24 11:27:09,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cbe5675-bcca-4766-9cb2-dd5c021950d3/GCF_011761445.1_ASM1176144v1_genomic.fna.gz --refList GCF_011761445.1_ASM1176144v1_genomic.fna/target_genomes.txt --output GCF_011761445.1_ASM1176144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:17,749] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:17,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:17,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:17,763] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:27:17,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:17,764] [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=CECT 8354	GCA_011761445.1	1526412	1526412	type	True	100.0	963	965	95	conclusive
Microbacterium endophyticum	strain=DSM 27099	GCA_011047135.1	1526412	1526412	type	True	99.9968	965	965	95	conclusive
Microbacterium endophyticum	strain=DSM 27099	GCA_014191465.1	1526412	1526412	type	True	99.9931	941	965	95	conclusive
Microbacterium halimionae	strain=CECT 8593	GCA_011761265.1	1526413	1526413	type	True	85.9212	711	965	95	below_threshold
Microbacterium halimionae	strain=DSM 27576	GCA_014137985.1	1526413	1526413	type	True	85.9131	715	965	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	77.9211	221	965	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	77.899	219	965	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	77.0889	97	965	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.0689	149	965	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	76.9424	136	965	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	76.2544	51	965	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.1264	53	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:17,767] [INFO] DFAST Taxonomy check result was written to GCF_011761445.1_ASM1176144v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:17,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:17,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:17,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference/checkm_data
[2024-01-24 11:27:17,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:17,797] [INFO] Task started: CheckM
[2024-01-24 11:27:17,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761445.1_ASM1176144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761445.1_ASM1176144v1_genomic.fna/checkm_input GCF_011761445.1_ASM1176144v1_genomic.fna/checkm_result
[2024-01-24 11:27:51,152] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:51,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,177] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:51,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:51,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761445.1_ASM1176144v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:51,179] [INFO] Task started: Blastn
[2024-01-24 11:27:51,179] [INFO] Running command: blastn -query GCF_011761445.1_ASM1176144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga196506e-6b23-4401-a35c-bb2f8841d844/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761445.1_ASM1176144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:52,533] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:52,538] [INFO] Selected 22 target genomes.
[2024-01-24 11:27:52,538] [INFO] Target genome list was writen to GCF_011761445.1_ASM1176144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:52,562] [INFO] Task started: fastANI
[2024-01-24 11:27:52,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cbe5675-bcca-4766-9cb2-dd5c021950d3/GCF_011761445.1_ASM1176144v1_genomic.fna.gz --refList GCF_011761445.1_ASM1176144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761445.1_ASM1176144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:05,007] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:05,029] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:05,029] [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	99.9968	965	965	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	85.9212	711	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001427525.1	s__Microbacterium sp001427525	78.1484	240	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991875.1	s__Microbacterium lemovicicum	78.1293	229	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	78.0978	244	965	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	78.0874	204	965	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	78.0811	244	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828185.1	s__Microbacterium sp007828185	78.0501	213	965	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	78.0476	258	965	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	78.0139	226	965	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	77.9932	220	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCF_003635115.1	s__Microbacterium sp003635115	77.9902	252	965	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	77.974	237	965	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	77.9627	229	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_012847295.1	s__Microbacterium sp012847295	77.9286	221	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014197265.1	s__Microbacterium invictum	77.9285	218	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004564355.1	s__Microbacterium wangchenii	77.8717	225	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.29	98.90	0.96	0.95	3	-
GCF_900292075.1	s__Microbacterium timonense	77.8306	224	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	77.76	277	965	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	77.6468	232	965	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	77.6097	222	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017968845.1	s__Microbacterium sp017968845	77.5651	166	965	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 11:28:05,031] [INFO] GTDB search result was written to GCF_011761445.1_ASM1176144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:05,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:05,035] [INFO] DFAST_QC result json was written to GCF_011761445.1_ASM1176144v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:05,035] [INFO] DFAST_QC completed!
[2024-01-24 11:28:05,035] [INFO] Total running time: 0h1m11s