[2023-06-08 07:23:41,593] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:23:41,599] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:23:41,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference
[2023-06-08 07:23:43,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:23:43,094] [INFO] Task started: Prodigal
[2023-06-08 07:23:43,094] [INFO] Running command: gunzip -c /var/lib/cwl/stgf12cacdf-aafc-471e-a601-2ed9da6d2b40/GCA_000989785.1_ASM98978v1_genomic.fna.gz | prodigal -d GCA_000989785.1_ASM98978v1_genomic.fna/cds.fna -a GCA_000989785.1_ASM98978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:23:45,526] [INFO] Task succeeded: Prodigal
[2023-06-08 07:23:45,527] [INFO] Task started: HMMsearch
[2023-06-08 07:23:45,527] [INFO] Running command: hmmsearch --tblout GCA_000989785.1_ASM98978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference/reference_markers.hmm GCA_000989785.1_ASM98978v1_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:23:45,703] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:23:45,704] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf12cacdf-aafc-471e-a601-2ed9da6d2b40/GCA_000989785.1_ASM98978v1_genomic.fna.gz]
[2023-06-08 07:23:45,721] [INFO] Query marker FASTA was written to GCA_000989785.1_ASM98978v1_genomic.fna/markers.fasta
[2023-06-08 07:23:45,722] [INFO] Task started: Blastn
[2023-06-08 07:23:45,722] [INFO] Running command: blastn -query GCA_000989785.1_ASM98978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference/reference_markers.fasta -out GCA_000989785.1_ASM98978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:23:46,275] [INFO] Task succeeded: Blastn
[2023-06-08 07:23:46,279] [INFO] Selected 11 target genomes.
[2023-06-08 07:23:46,280] [INFO] Target genome list was writen to GCA_000989785.1_ASM98978v1_genomic.fna/target_genomes.txt
[2023-06-08 07:23:46,281] [INFO] Task started: fastANI
[2023-06-08 07:23:46,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12cacdf-aafc-471e-a601-2ed9da6d2b40/GCA_000989785.1_ASM98978v1_genomic.fna.gz --refList GCA_000989785.1_ASM98978v1_genomic.fna/target_genomes.txt --output GCA_000989785.1_ASM98978v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:23:51,304] [INFO] Task succeeded: fastANI
[2023-06-08 07:23:51,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:23:51,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:23:51,306] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:23:51,306] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:23:51,306] [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
--------------------------------------------------------------------------------
[2023-06-08 07:23:51,308] [INFO] DFAST Taxonomy check result was written to GCA_000989785.1_ASM98978v1_genomic.fna/tc_result.tsv
[2023-06-08 07:23:51,309] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:23:51,309] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:23:51,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference/checkm_data
[2023-06-08 07:23:51,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:23:51,327] [INFO] Task started: CheckM
[2023-06-08 07:23:51,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_000989785.1_ASM98978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_000989785.1_ASM98978v1_genomic.fna/checkm_input GCA_000989785.1_ASM98978v1_genomic.fna/checkm_result
[2023-06-08 07:24:06,800] [INFO] Task succeeded: CheckM
[2023-06-08 07:24:06,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:24:06,824] [INFO] ===== Completeness check finished =====
[2023-06-08 07:24:06,825] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:24:06,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_000989785.1_ASM98978v1_genomic.fna/markers.fasta)
[2023-06-08 07:24:06,826] [INFO] Task started: Blastn
[2023-06-08 07:24:06,826] [INFO] Running command: blastn -query GCA_000989785.1_ASM98978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30433bf1-99de-4d86-9e58-a4aa1a42b350/dqc_reference/reference_markers_gtdb.fasta -out GCA_000989785.1_ASM98978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:07,279] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:07,283] [INFO] Selected 11 target genomes.
[2023-06-08 07:24:07,284] [INFO] Target genome list was writen to GCA_000989785.1_ASM98978v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:24:07,285] [INFO] Task started: fastANI
[2023-06-08 07:24:07,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12cacdf-aafc-471e-a601-2ed9da6d2b40/GCA_000989785.1_ASM98978v1_genomic.fna.gz --refList GCA_000989785.1_ASM98978v1_genomic.fna/target_genomes_gtdb.txt --output GCA_000989785.1_ASM98978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:24:10,779] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:10,784] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:24:10,784] [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_001782645.1	s__GWB1-37-8 sp001782645	99.5687	143	188	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__Levybacterales;f__UBA12049;g__GWB1-37-8	95.0	99.62	99.59	0.82	0.82	3	conclusive
GCA_001783805.1	s__GWB1-37-8 sp001783805	78.8745	83	188	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__Levybacterales;f__UBA12049;g__GWB1-37-8	95.0	99.96	99.94	0.99	0.98	3	-
GCA_016186645.1	s__GWB1-37-8 sp016186645	77.1428	52	188	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__Levybacterales;f__UBA12049;g__GWB1-37-8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:24:10,786] [INFO] GTDB search result was written to GCA_000989785.1_ASM98978v1_genomic.fna/result_gtdb.tsv
[2023-06-08 07:24:10,786] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:24:10,789] [INFO] DFAST_QC result json was written to GCA_000989785.1_ASM98978v1_genomic.fna/dqc_result.json
[2023-06-08 07:24:10,790] [INFO] DFAST_QC completed!
[2023-06-08 07:24:10,790] [INFO] Total running time: 0h0m29s