[2023-06-05 12:22:32,214] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:22:32,219] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:22:32,219] [INFO] DQC Reference Directory: /var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference
[2023-06-05 12:22:33,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:22:33,807] [INFO] Task started: Prodigal
[2023-06-05 12:22:33,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f837b31-9fff-4c7d-b47f-f418dc4678d1/GCA_010022465.1_ASM1002246v1_genomic.fna.gz | prodigal -d GCA_010022465.1_ASM1002246v1_genomic.fna/cds.fna -a GCA_010022465.1_ASM1002246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:22:37,217] [INFO] Task succeeded: Prodigal
[2023-06-05 12:22:37,218] [INFO] Task started: HMMsearch
[2023-06-05 12:22:37,218] [INFO] Running command: hmmsearch --tblout GCA_010022465.1_ASM1002246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference/reference_markers.hmm GCA_010022465.1_ASM1002246v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:22:37,373] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:22:37,374] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f837b31-9fff-4c7d-b47f-f418dc4678d1/GCA_010022465.1_ASM1002246v1_genomic.fna.gz]
[2023-06-05 12:22:37,390] [INFO] Query marker FASTA was written to GCA_010022465.1_ASM1002246v1_genomic.fna/markers.fasta
[2023-06-05 12:22:37,390] [INFO] Task started: Blastn
[2023-06-05 12:22:37,390] [INFO] Running command: blastn -query GCA_010022465.1_ASM1002246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference/reference_markers.fasta -out GCA_010022465.1_ASM1002246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:22:37,912] [INFO] Task succeeded: Blastn
[2023-06-05 12:22:37,915] [INFO] Selected 19 target genomes.
[2023-06-05 12:22:37,916] [INFO] Target genome list was writen to GCA_010022465.1_ASM1002246v1_genomic.fna/target_genomes.txt
[2023-06-05 12:22:37,918] [INFO] Task started: fastANI
[2023-06-05 12:22:37,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f837b31-9fff-4c7d-b47f-f418dc4678d1/GCA_010022465.1_ASM1002246v1_genomic.fna.gz --refList GCA_010022465.1_ASM1002246v1_genomic.fna/target_genomes.txt --output GCA_010022465.1_ASM1002246v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:22:49,746] [INFO] Task succeeded: fastANI
[2023-06-05 12:22:49,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:22:49,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:22:49,749] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:22:49,749] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 12:22:49,749] [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
--------------------------------------------------------------------------------
[2023-06-05 12:22:49,751] [INFO] DFAST Taxonomy check result was written to GCA_010022465.1_ASM1002246v1_genomic.fna/tc_result.tsv
[2023-06-05 12:22:49,752] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:22:49,752] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:22:49,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference/checkm_data
[2023-06-05 12:22:49,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:22:49,772] [INFO] Task started: CheckM
[2023-06-05 12:22:49,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010022465.1_ASM1002246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010022465.1_ASM1002246v1_genomic.fna/checkm_input GCA_010022465.1_ASM1002246v1_genomic.fna/checkm_result
[2023-06-05 12:23:07,990] [INFO] Task succeeded: CheckM
[2023-06-05 12:23:07,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.97%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:23:08,012] [INFO] ===== Completeness check finished =====
[2023-06-05 12:23:08,013] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:23:08,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010022465.1_ASM1002246v1_genomic.fna/markers.fasta)
[2023-06-05 12:23:08,013] [INFO] Task started: Blastn
[2023-06-05 12:23:08,013] [INFO] Running command: blastn -query GCA_010022465.1_ASM1002246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1c7096e-672a-4ad9-9394-51926cf04ba7/dqc_reference/reference_markers_gtdb.fasta -out GCA_010022465.1_ASM1002246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:23:08,577] [INFO] Task succeeded: Blastn
[2023-06-05 12:23:08,580] [INFO] Selected 11 target genomes.
[2023-06-05 12:23:08,581] [INFO] Target genome list was writen to GCA_010022465.1_ASM1002246v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:23:08,584] [INFO] Task started: fastANI
[2023-06-05 12:23:08,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f837b31-9fff-4c7d-b47f-f418dc4678d1/GCA_010022465.1_ASM1002246v1_genomic.fna.gz --refList GCA_010022465.1_ASM1002246v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010022465.1_ASM1002246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:23:11,641] [INFO] Task succeeded: fastANI
[2023-06-05 12:23:11,649] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:23:11,649] [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_010025655.1	s__F1-60-MAGs027 sp010025655	97.725	136	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	98.35	98.13	0.74	0.70	11	conclusive
GCA_009927665.1	s__F1-60-MAGs027 sp009927665	84.4006	142	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	99.21	99.09	0.94	0.94	3	-
GCA_009926705.1	s__F1-60-MAGs027 sp009926705	79.7745	60	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856115.1	s__F1-60-MAGs027 sp017856115	78.1053	66	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853375.1	s__F1-60-MAGs027 sp017853375	77.7571	61	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463775.1	s__F1-60-MAGs027 sp016463775	77.4609	72	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005793215.1	s__F1-60-MAGs027 sp005793215	77.2327	55	170	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	98.97	98.30	0.86	0.85	4	-
--------------------------------------------------------------------------------
[2023-06-05 12:23:11,651] [INFO] GTDB search result was written to GCA_010022465.1_ASM1002246v1_genomic.fna/result_gtdb.tsv
[2023-06-05 12:23:11,652] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:23:11,654] [INFO] DFAST_QC result json was written to GCA_010022465.1_ASM1002246v1_genomic.fna/dqc_result.json
[2023-06-05 12:23:11,654] [INFO] DFAST_QC completed!
[2023-06-05 12:23:11,655] [INFO] Total running time: 0h0m39s