[2024-01-24 13:58:10,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference
[2024-01-24 13:58:11,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,995] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg8072279f-a87b-41a3-a7a0-16cec1771460/GCF_002936985.1_ASM293698v1_genomic.fna.gz | prodigal -d GCF_002936985.1_ASM293698v1_genomic.fna/cds.fna -a GCF_002936985.1_ASM293698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:22,364] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:22,364] [INFO] Task started: HMMsearch
[2024-01-24 13:58:22,364] [INFO] Running command: hmmsearch --tblout GCF_002936985.1_ASM293698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference/reference_markers.hmm GCF_002936985.1_ASM293698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:22,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:22,631] [INFO] Found 6/6 markers.
[2024-01-24 13:58:22,666] [INFO] Query marker FASTA was written to GCF_002936985.1_ASM293698v1_genomic.fna/markers.fasta
[2024-01-24 13:58:22,667] [INFO] Task started: Blastn
[2024-01-24 13:58:22,667] [INFO] Running command: blastn -query GCF_002936985.1_ASM293698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference/reference_markers.fasta -out GCF_002936985.1_ASM293698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:23,992] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:23,998] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:23,999] [INFO] Target genome list was writen to GCF_002936985.1_ASM293698v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,005] [INFO] Task started: fastANI
[2024-01-24 13:58:24,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg8072279f-a87b-41a3-a7a0-16cec1771460/GCF_002936985.1_ASM293698v1_genomic.fna.gz --refList GCF_002936985.1_ASM293698v1_genomic.fna/target_genomes.txt --output GCF_002936985.1_ASM293698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:38,277] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:38,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:38,299] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:38,299] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:38,299] [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
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	100.0	1150	1158	95	inconclusive
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	96.4039	1048	1158	95	inconclusive
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	85.0837	813	1158	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	80.291	451	1158	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	80.2768	450	1158	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	80.0847	504	1158	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	80.0624	547	1158	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	79.9888	373	1158	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.9272	518	1158	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.8389	558	1158	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	79.7859	525	1158	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.7622	492	1158	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	79.743	540	1158	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	79.3672	539	1158	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	79.2535	511	1158	95	below_threshold
Mycetocola miduiensis	strain=CGMCC 1.11101	GCA_900115155.1	995034	995034	type	True	79.0656	335	1158	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.9741	423	1158	95	below_threshold
Mycetocola manganoxydans	strain=KCTC 19753	GCA_014651755.1	699879	699879	type	True	78.8515	335	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,301] [INFO] DFAST Taxonomy check result was written to GCF_002936985.1_ASM293698v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:38,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:38,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:38,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference/checkm_data
[2024-01-24 13:58:38,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:38,342] [INFO] Task started: CheckM
[2024-01-24 13:58:38,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002936985.1_ASM293698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002936985.1_ASM293698v1_genomic.fna/checkm_input GCF_002936985.1_ASM293698v1_genomic.fna/checkm_result
[2024-01-24 13:59:11,662] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:11,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,682] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:11,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:11,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002936985.1_ASM293698v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:11,684] [INFO] Task started: Blastn
[2024-01-24 13:59:11,684] [INFO] Running command: blastn -query GCF_002936985.1_ASM293698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e949422-e40d-473c-ac55-d1bc07b9f6fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002936985.1_ASM293698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:13,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:13,867] [INFO] Selected 6 target genomes.
[2024-01-24 13:59:13,867] [INFO] Target genome list was writen to GCF_002936985.1_ASM293698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:13,876] [INFO] Task started: fastANI
[2024-01-24 13:59:13,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg8072279f-a87b-41a3-a7a0-16cec1771460/GCF_002936985.1_ASM293698v1_genomic.fna.gz --refList GCF_002936985.1_ASM293698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002936985.1_ASM293698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,708] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,715] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,715] [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_002936985.1	s__Microterricola pindariensis	100.0	1150	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104895.1	s__Microterricola viridarii	96.4039	1048	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	conclusive
GCF_001542775.1	s__Microterricola viridarii_A	89.0503	956	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217495.1	s__Microterricola gilva	85.0614	815	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425085.1	s__Microterricola sp001425085	85.0203	807	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610585.1	s__Microterricola sp003610585	84.9851	799	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,717] [INFO] GTDB search result was written to GCF_002936985.1_ASM293698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,718] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,721] [INFO] DFAST_QC result json was written to GCF_002936985.1_ASM293698v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,721] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,721] [INFO] Total running time: 0h1m10s