[2024-01-24 13:17:25,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:25,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:25,351] [INFO] DQC Reference Directory: /var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference
[2024-01-24 13:17:26,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:26,750] [INFO] Task started: Prodigal
[2024-01-24 13:17:26,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg695fefa2-6ddb-41b2-937c-08860f7d17a5/GCF_000230655.2_ASM23065v3_genomic.fna.gz | prodigal -d GCF_000230655.2_ASM23065v3_genomic.fna/cds.fna -a GCF_000230655.2_ASM23065v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:31,800] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:31,801] [INFO] Task started: HMMsearch
[2024-01-24 13:17:31,801] [INFO] Running command: hmmsearch --tblout GCF_000230655.2_ASM23065v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference/reference_markers.hmm GCF_000230655.2_ASM23065v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:32,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:32,129] [INFO] Found 6/6 markers.
[2024-01-24 13:17:32,162] [INFO] Query marker FASTA was written to GCF_000230655.2_ASM23065v3_genomic.fna/markers.fasta
[2024-01-24 13:17:32,169] [INFO] Task started: Blastn
[2024-01-24 13:17:32,169] [INFO] Running command: blastn -query GCF_000230655.2_ASM23065v3_genomic.fna/markers.fasta -db /var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference/reference_markers.fasta -out GCF_000230655.2_ASM23065v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:32,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:32,763] [INFO] Selected 5 target genomes.
[2024-01-24 13:17:32,763] [INFO] Target genome list was writen to GCF_000230655.2_ASM23065v3_genomic.fna/target_genomes.txt
[2024-01-24 13:17:32,766] [INFO] Task started: fastANI
[2024-01-24 13:17:32,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg695fefa2-6ddb-41b2-937c-08860f7d17a5/GCF_000230655.2_ASM23065v3_genomic.fna.gz --refList GCF_000230655.2_ASM23065v3_genomic.fna/target_genomes.txt --output GCF_000230655.2_ASM23065v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:35,114] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:35,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:35,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:35,122] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:17:35,122] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:17:35,122] [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
Thermotoga maritima	strain=MSB8	GCA_000230655.3	2336	2336	type	True	100.0	622	623	95	inconclusive
Thermotoga maritima	strain=MSB8	GCA_000978555.1	2336	2336	type	True	99.9964	623	623	95	inconclusive
Thermotoga maritima	strain=MSB8	GCA_000390265.1	2336	2336	type	True	99.9962	623	623	95	inconclusive
Thermotoga maritima	strain=MSB8	GCA_000008545.1	2336	2336	type	True	99.9908	620	623	95	inconclusive
Thermotoga petrophila	strain=RKU-1	GCA_000016785.1	93929	93929	type	True	95.1969	564	623	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:35,124] [INFO] DFAST Taxonomy check result was written to GCF_000230655.2_ASM23065v3_genomic.fna/tc_result.tsv
[2024-01-24 13:17:35,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:35,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:35,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference/checkm_data
[2024-01-24 13:17:35,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:35,154] [INFO] Task started: CheckM
[2024-01-24 13:17:35,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000230655.2_ASM23065v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000230655.2_ASM23065v3_genomic.fna/checkm_input GCF_000230655.2_ASM23065v3_genomic.fna/checkm_result
[2024-01-24 13:17:58,608] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:58,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,627] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:58,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:58,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000230655.2_ASM23065v3_genomic.fna/markers.fasta)
[2024-01-24 13:17:58,629] [INFO] Task started: Blastn
[2024-01-24 13:17:58,629] [INFO] Running command: blastn -query GCF_000230655.2_ASM23065v3_genomic.fna/markers.fasta -db /var/lib/cwl/stge3cae3a1-ffdf-466f-995e-a32501f05527/dqc_reference/reference_markers_gtdb.fasta -out GCF_000230655.2_ASM23065v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:59,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:59,443] [INFO] Selected 8 target genomes.
[2024-01-24 13:17:59,443] [INFO] Target genome list was writen to GCF_000230655.2_ASM23065v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:59,451] [INFO] Task started: fastANI
[2024-01-24 13:17:59,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg695fefa2-6ddb-41b2-937c-08860f7d17a5/GCF_000230655.2_ASM23065v3_genomic.fna.gz --refList GCF_000230655.2_ASM23065v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000230655.2_ASM23065v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:02,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,592] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:02,592] [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_000008545.1	s__Thermotoga maritima	99.9908	620	623	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.1972	98.60	96.82	0.97	0.93	11	conclusive
GCF_000016785.1	s__Thermotoga petrophila	95.1969	564	623	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.1972	97.11	96.82	0.93	0.85	13	-
GCF_000784835.1	s__Thermotoga sp000784835	93.9083	573	623	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	97.67	97.67	0.94	0.94	2	-
GCF_000018945.1	s__Thermotoga neapolitana	83.0358	399	623	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	99.53	98.63	0.97	0.93	4	-
GCF_002865985.1	s__Thermotoga sp002865985	79.6489	351	623	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,594] [INFO] GTDB search result was written to GCF_000230655.2_ASM23065v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:02,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:02,599] [INFO] DFAST_QC result json was written to GCF_000230655.2_ASM23065v3_genomic.fna/dqc_result.json
[2024-01-24 13:18:02,600] [INFO] DFAST_QC completed!
[2024-01-24 13:18:02,600] [INFO] Total running time: 0h0m37s