[2023-06-27 17:41:04,873] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:04,879] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:04,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference
[2023-06-27 17:41:06,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:06,128] [INFO] Task started: Prodigal
[2023-06-27 17:41:06,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg13878966-5bf3-4170-9155-7139ef5038b5/GCA_002331465.1_ASM233146v1_genomic.fna.gz | prodigal -d GCA_002331465.1_ASM233146v1_genomic.fna/cds.fna -a GCA_002331465.1_ASM233146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:11,699] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:11,700] [INFO] Task started: HMMsearch
[2023-06-27 17:41:11,700] [INFO] Running command: hmmsearch --tblout GCA_002331465.1_ASM233146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference/reference_markers.hmm GCA_002331465.1_ASM233146v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:11,863] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:11,864] [INFO] Found 6/6 markers.
[2023-06-27 17:41:11,887] [INFO] Query marker FASTA was written to GCA_002331465.1_ASM233146v1_genomic.fna/markers.fasta
[2023-06-27 17:41:11,887] [INFO] Task started: Blastn
[2023-06-27 17:41:11,888] [INFO] Running command: blastn -query GCA_002331465.1_ASM233146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference/reference_markers.fasta -out GCA_002331465.1_ASM233146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:12,421] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:12,424] [INFO] Selected 16 target genomes.
[2023-06-27 17:41:12,425] [INFO] Target genome list was writen to GCA_002331465.1_ASM233146v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:12,429] [INFO] Task started: fastANI
[2023-06-27 17:41:12,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg13878966-5bf3-4170-9155-7139ef5038b5/GCA_002331465.1_ASM233146v1_genomic.fna.gz --refList GCA_002331465.1_ASM233146v1_genomic.fna/target_genomes.txt --output GCA_002331465.1_ASM233146v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:19,971] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:19,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:19,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:19,973] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:41:19,973] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 17:41:19,973] [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
--------------------------------------------------------------------------------
[2023-06-27 17:41:19,976] [INFO] DFAST Taxonomy check result was written to GCA_002331465.1_ASM233146v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:19,977] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:19,977] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:19,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference/checkm_data
[2023-06-27 17:41:19,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:20,006] [INFO] Task started: CheckM
[2023-06-27 17:41:20,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002331465.1_ASM233146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002331465.1_ASM233146v1_genomic.fna/checkm_input GCA_002331465.1_ASM233146v1_genomic.fna/checkm_result
[2023-06-27 17:41:42,318] [INFO] Task succeeded: CheckM
[2023-06-27 17:41:42,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:41:42,335] [INFO] ===== Completeness check finished =====
[2023-06-27 17:41:42,336] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:41:42,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002331465.1_ASM233146v1_genomic.fna/markers.fasta)
[2023-06-27 17:41:42,336] [INFO] Task started: Blastn
[2023-06-27 17:41:42,336] [INFO] Running command: blastn -query GCA_002331465.1_ASM233146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0531ce29-d921-40a4-98d3-1221794f4ef7/dqc_reference/reference_markers_gtdb.fasta -out GCA_002331465.1_ASM233146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:43,016] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:43,020] [INFO] Selected 11 target genomes.
[2023-06-27 17:41:43,020] [INFO] Target genome list was writen to GCA_002331465.1_ASM233146v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:41:43,026] [INFO] Task started: fastANI
[2023-06-27 17:41:43,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg13878966-5bf3-4170-9155-7139ef5038b5/GCA_002331465.1_ASM233146v1_genomic.fna.gz --refList GCA_002331465.1_ASM233146v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002331465.1_ASM233146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:41:47,941] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:47,947] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:41:47,947] [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
GCA_002331465.1	s__UBA2110 sp002331465	99.9999	648	672	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012960315.1	s__UBA2110 sp012960315	94.0234	611	672	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	-
GCA_014239555.1	s__UBA2110 sp014239555	90.2027	634	672	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719335.1	s__UBA2110 sp002719335	84.3743	480	672	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	96.75	96.75	0.83	0.83	2	-
GCA_002388005.1	s__UBA2110 sp002388005	79.0964	332	672	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705305.1	s__UBA2110 sp002705305	78.7455	294	672	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 17:41:47,949] [INFO] GTDB search result was written to GCA_002331465.1_ASM233146v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:41:47,950] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:41:47,952] [INFO] DFAST_QC result json was written to GCA_002331465.1_ASM233146v1_genomic.fna/dqc_result.json
[2023-06-27 17:41:47,952] [INFO] DFAST_QC completed!
[2023-06-27 17:41:47,952] [INFO] Total running time: 0h0m43s