[2024-01-24 12:15:20,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference
[2024-01-24 12:15:22,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,044] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ae56b83-5ccd-4d08-b246-7fe7bf6161a6/GCF_020042345.1_ASM2004234v1_genomic.fna.gz | prodigal -d GCF_020042345.1_ASM2004234v1_genomic.fna/cds.fna -a GCF_020042345.1_ASM2004234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:43,740] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:43,740] [INFO] Task started: HMMsearch
[2024-01-24 12:15:43,740] [INFO] Running command: hmmsearch --tblout GCF_020042345.1_ASM2004234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference/reference_markers.hmm GCF_020042345.1_ASM2004234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:44,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:44,044] [INFO] Found 6/6 markers.
[2024-01-24 12:15:44,091] [INFO] Query marker FASTA was written to GCF_020042345.1_ASM2004234v1_genomic.fna/markers.fasta
[2024-01-24 12:15:44,092] [INFO] Task started: Blastn
[2024-01-24 12:15:44,092] [INFO] Running command: blastn -query GCF_020042345.1_ASM2004234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference/reference_markers.fasta -out GCF_020042345.1_ASM2004234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:44,674] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:44,678] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:44,679] [INFO] Target genome list was writen to GCF_020042345.1_ASM2004234v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:44,687] [INFO] Task started: fastANI
[2024-01-24 12:15:44,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ae56b83-5ccd-4d08-b246-7fe7bf6161a6/GCF_020042345.1_ASM2004234v1_genomic.fna.gz --refList GCF_020042345.1_ASM2004234v1_genomic.fna/target_genomes.txt --output GCF_020042345.1_ASM2004234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:02,730] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:02,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:02,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:02,738] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:02,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:02,738] [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
Arachidicoccus terrestris	strain=5GH13-10	GCA_020042345.1	2875539	2875539	type	True	100.0	1632	1633	95	conclusive
Arachidicoccus ginsenosidivorans	strain=Gsoil 809	GCA_007971385.1	496057	496057	type	True	79.2881	530	1633	95	below_threshold
Arachidicoccus rhizosphaerae	strain=Vu-144	GCA_900107765.1	551991	551991	type	True	79.0572	497	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,740] [INFO] DFAST Taxonomy check result was written to GCF_020042345.1_ASM2004234v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:02,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:02,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:02,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference/checkm_data
[2024-01-24 12:16:02,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:02,789] [INFO] Task started: CheckM
[2024-01-24 12:16:02,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020042345.1_ASM2004234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020042345.1_ASM2004234v1_genomic.fna/checkm_input GCF_020042345.1_ASM2004234v1_genomic.fna/checkm_result
[2024-01-24 12:17:03,765] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:03,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:03,790] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:03,790] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:03,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020042345.1_ASM2004234v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:03,791] [INFO] Task started: Blastn
[2024-01-24 12:17:03,791] [INFO] Running command: blastn -query GCF_020042345.1_ASM2004234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53651456-e801-47ec-85ad-77fd63f43e95/dqc_reference/reference_markers_gtdb.fasta -out GCF_020042345.1_ASM2004234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:04,550] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:04,553] [INFO] Selected 27 target genomes.
[2024-01-24 12:17:04,553] [INFO] Target genome list was writen to GCF_020042345.1_ASM2004234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:04,608] [INFO] Task started: fastANI
[2024-01-24 12:17:04,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ae56b83-5ccd-4d08-b246-7fe7bf6161a6/GCF_020042345.1_ASM2004234v1_genomic.fna.gz --refList GCF_020042345.1_ASM2004234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020042345.1_ASM2004234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:24,291] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:24,298] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:24,298] [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_007971385.1	s__Arachidicoccus ginsenosidivorans	79.2729	529	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107765.1	s__Arachidicoccus rhizosphaerae	79.0656	496	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659705.1	s__Arachidicoccus sp001659705	76.7614	62	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Arachidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:24,299] [INFO] GTDB search result was written to GCF_020042345.1_ASM2004234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:24,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:24,302] [INFO] DFAST_QC result json was written to GCF_020042345.1_ASM2004234v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:24,303] [INFO] DFAST_QC completed!
[2024-01-24 12:17:24,303] [INFO] Total running time: 0h2m4s