[2023-06-28 19:48:04,133] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:04,136] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:04,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference
[2023-06-28 19:48:05,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:05,629] [INFO] Task started: Prodigal
[2023-06-28 19:48:05,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg7077926e-4f9f-4751-b160-0113d2a5a280/GCA_019310695.1_ASM1931069v1_genomic.fna.gz | prodigal -d GCA_019310695.1_ASM1931069v1_genomic.fna/cds.fna -a GCA_019310695.1_ASM1931069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:11,664] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:11,664] [INFO] Task started: HMMsearch
[2023-06-28 19:48:11,664] [INFO] Running command: hmmsearch --tblout GCA_019310695.1_ASM1931069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference/reference_markers.hmm GCA_019310695.1_ASM1931069v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:11,912] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:11,914] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7077926e-4f9f-4751-b160-0113d2a5a280/GCA_019310695.1_ASM1931069v1_genomic.fna.gz]
[2023-06-28 19:48:11,941] [INFO] Query marker FASTA was written to GCA_019310695.1_ASM1931069v1_genomic.fna/markers.fasta
[2023-06-28 19:48:11,941] [INFO] Task started: Blastn
[2023-06-28 19:48:11,941] [INFO] Running command: blastn -query GCA_019310695.1_ASM1931069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference/reference_markers.fasta -out GCA_019310695.1_ASM1931069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:12,504] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:12,509] [INFO] Selected 13 target genomes.
[2023-06-28 19:48:12,509] [INFO] Target genome list was writen to GCA_019310695.1_ASM1931069v1_genomic.fna/target_genomes.txt
[2023-06-28 19:48:12,512] [INFO] Task started: fastANI
[2023-06-28 19:48:12,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg7077926e-4f9f-4751-b160-0113d2a5a280/GCA_019310695.1_ASM1931069v1_genomic.fna.gz --refList GCA_019310695.1_ASM1931069v1_genomic.fna/target_genomes.txt --output GCA_019310695.1_ASM1931069v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:21,068] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:21,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:21,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:21,071] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:21,071] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:48:21,072] [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
--------------------------------------------------------------------------------
[2023-06-28 19:48:21,074] [INFO] DFAST Taxonomy check result was written to GCA_019310695.1_ASM1931069v1_genomic.fna/tc_result.tsv
[2023-06-28 19:48:21,075] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:21,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:21,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference/checkm_data
[2023-06-28 19:48:21,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:21,110] [INFO] Task started: CheckM
[2023-06-28 19:48:21,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310695.1_ASM1931069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310695.1_ASM1931069v1_genomic.fna/checkm_input GCA_019310695.1_ASM1931069v1_genomic.fna/checkm_result
[2023-06-28 19:48:46,127] [INFO] Task succeeded: CheckM
[2023-06-28 19:48:46,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.36%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:48:46,153] [INFO] ===== Completeness check finished =====
[2023-06-28 19:48:46,153] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:48:46,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310695.1_ASM1931069v1_genomic.fna/markers.fasta)
[2023-06-28 19:48:46,154] [INFO] Task started: Blastn
[2023-06-28 19:48:46,154] [INFO] Running command: blastn -query GCA_019310695.1_ASM1931069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9232fb8d-3228-470b-958d-80da8c460cdb/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310695.1_ASM1931069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:46,919] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:46,923] [INFO] Selected 14 target genomes.
[2023-06-28 19:48:46,924] [INFO] Target genome list was writen to GCA_019310695.1_ASM1931069v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:48:46,932] [INFO] Task started: fastANI
[2023-06-28 19:48:46,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg7077926e-4f9f-4751-b160-0113d2a5a280/GCA_019310695.1_ASM1931069v1_genomic.fna.gz --refList GCA_019310695.1_ASM1931069v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310695.1_ASM1931069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:48:54,268] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:54,278] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:48:54,278] [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_003647275.1	s__B60-G16 sp003647275	80.664	314	739	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__C00003060;f__C00003060;g__B60-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001751085.1	s__C00003060 sp001751085	80.5926	232	739	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__C00003060;f__C00003060;g__C00003060	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013375375.1	s__JABXJX01 sp013375375	80.535	259	739	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__C00003060;f__C00003060;g__JABXJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003647435.1	s__B23-G16 sp003647435	76.4619	50	739	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__C00003060;f__C00003060;g__B23-G16	95.0	97.43	97.43	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-06-28 19:48:54,281] [INFO] GTDB search result was written to GCA_019310695.1_ASM1931069v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:48:54,281] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:48:54,284] [INFO] DFAST_QC result json was written to GCA_019310695.1_ASM1931069v1_genomic.fna/dqc_result.json
[2023-06-28 19:48:54,284] [INFO] DFAST_QC completed!
[2023-06-28 19:48:54,284] [INFO] Total running time: 0h0m50s