[2023-06-16 20:52:43,783] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:52:43,785] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:52:43,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference
[2023-06-16 20:52:45,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:52:45,058] [INFO] Task started: Prodigal
[2023-06-16 20:52:45,058] [INFO] Running command: gunzip -c /var/lib/cwl/stga92456c1-1ac5-4b3e-bfbc-49a24d8820ea/GCA_009700115.1_ASM970011v1_genomic.fna.gz | prodigal -d GCA_009700115.1_ASM970011v1_genomic.fna/cds.fna -a GCA_009700115.1_ASM970011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:52:50,852] [INFO] Task succeeded: Prodigal
[2023-06-16 20:52:50,853] [INFO] Task started: HMMsearch
[2023-06-16 20:52:50,853] [INFO] Running command: hmmsearch --tblout GCA_009700115.1_ASM970011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference/reference_markers.hmm GCA_009700115.1_ASM970011v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:52:51,036] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:52:51,037] [INFO] Found 6/6 markers.
[2023-06-16 20:52:51,062] [INFO] Query marker FASTA was written to GCA_009700115.1_ASM970011v1_genomic.fna/markers.fasta
[2023-06-16 20:52:51,062] [INFO] Task started: Blastn
[2023-06-16 20:52:51,062] [INFO] Running command: blastn -query GCA_009700115.1_ASM970011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference/reference_markers.fasta -out GCA_009700115.1_ASM970011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:52:51,637] [INFO] Task succeeded: Blastn
[2023-06-16 20:52:51,644] [INFO] Selected 23 target genomes.
[2023-06-16 20:52:51,644] [INFO] Target genome list was writen to GCA_009700115.1_ASM970011v1_genomic.fna/target_genomes.txt
[2023-06-16 20:52:51,680] [INFO] Task started: fastANI
[2023-06-16 20:52:51,680] [INFO] Running command: fastANI --query /var/lib/cwl/stga92456c1-1ac5-4b3e-bfbc-49a24d8820ea/GCA_009700115.1_ASM970011v1_genomic.fna.gz --refList GCA_009700115.1_ASM970011v1_genomic.fna/target_genomes.txt --output GCA_009700115.1_ASM970011v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:53:07,108] [INFO] Task succeeded: fastANI
[2023-06-16 20:53:07,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:53:07,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:53:07,113] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:53:07,113] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:53:07,113] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8615	76	663	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:53:07,115] [INFO] DFAST Taxonomy check result was written to GCA_009700115.1_ASM970011v1_genomic.fna/tc_result.tsv
[2023-06-16 20:53:07,115] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:53:07,115] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:53:07,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference/checkm_data
[2023-06-16 20:53:07,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:53:07,141] [INFO] Task started: CheckM
[2023-06-16 20:53:07,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009700115.1_ASM970011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009700115.1_ASM970011v1_genomic.fna/checkm_input GCA_009700115.1_ASM970011v1_genomic.fna/checkm_result
[2023-06-16 20:53:28,768] [INFO] Task succeeded: CheckM
[2023-06-16 20:53:28,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:53:28,786] [INFO] ===== Completeness check finished =====
[2023-06-16 20:53:28,786] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:53:28,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009700115.1_ASM970011v1_genomic.fna/markers.fasta)
[2023-06-16 20:53:28,787] [INFO] Task started: Blastn
[2023-06-16 20:53:28,787] [INFO] Running command: blastn -query GCA_009700115.1_ASM970011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e4447e-94e8-43f1-b5bd-0b927091d706/dqc_reference/reference_markers_gtdb.fasta -out GCA_009700115.1_ASM970011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:53:29,640] [INFO] Task succeeded: Blastn
[2023-06-16 20:53:29,644] [INFO] Selected 6 target genomes.
[2023-06-16 20:53:29,644] [INFO] Target genome list was writen to GCA_009700115.1_ASM970011v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:53:29,648] [INFO] Task started: fastANI
[2023-06-16 20:53:29,648] [INFO] Running command: fastANI --query /var/lib/cwl/stga92456c1-1ac5-4b3e-bfbc-49a24d8820ea/GCA_009700115.1_ASM970011v1_genomic.fna.gz --refList GCA_009700115.1_ASM970011v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009700115.1_ASM970011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:53:32,370] [INFO] Task succeeded: fastANI
[2023-06-16 20:53:32,376] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:53:32,376] [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_009700115.1	s__F1-20-MAGs160 sp009700115	99.9999	652	663	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.37	98.87	0.88	0.85	10	conclusive
GCA_903867185.1	s__F1-20-MAGs160 sp903867185	89.6147	540	663	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462055.1	s__F1-20-MAGs160 sp016462055	87.5666	425	663	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827085.1	s__F1-20-MAGs160 sp903827085	81.3497	272	663	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699125.1	s__F1-20-MAGs160 sp009699125	80.7363	324	663	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.35	99.30	0.87	0.87	3	-
GCA_009703275.1	s__F1-20-MAGs160 sp009703275	80.408	279	663	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	98.87	98.58	0.79	0.77	4	-
--------------------------------------------------------------------------------
[2023-06-16 20:53:32,378] [INFO] GTDB search result was written to GCA_009700115.1_ASM970011v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:53:32,378] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:53:32,381] [INFO] DFAST_QC result json was written to GCA_009700115.1_ASM970011v1_genomic.fna/dqc_result.json
[2023-06-16 20:53:32,381] [INFO] DFAST_QC completed!
[2023-06-16 20:53:32,381] [INFO] Total running time: 0h0m49s