[2023-06-28 06:32:48,904] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:32:48,906] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:32:48,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference
[2023-06-28 06:32:50,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:32:50,083] [INFO] Task started: Prodigal
[2023-06-28 06:32:50,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dd8085b-c21d-4a0f-b9a4-f994a3f0a5e6/GCA_019310565.1_ASM1931056v1_genomic.fna.gz | prodigal -d GCA_019310565.1_ASM1931056v1_genomic.fna/cds.fna -a GCA_019310565.1_ASM1931056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:32:57,391] [INFO] Task succeeded: Prodigal
[2023-06-28 06:32:57,391] [INFO] Task started: HMMsearch
[2023-06-28 06:32:57,391] [INFO] Running command: hmmsearch --tblout GCA_019310565.1_ASM1931056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference/reference_markers.hmm GCA_019310565.1_ASM1931056v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:32:57,601] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:32:57,602] [INFO] Found 6/6 markers.
[2023-06-28 06:32:57,629] [INFO] Query marker FASTA was written to GCA_019310565.1_ASM1931056v1_genomic.fna/markers.fasta
[2023-06-28 06:32:57,630] [INFO] Task started: Blastn
[2023-06-28 06:32:57,630] [INFO] Running command: blastn -query GCA_019310565.1_ASM1931056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference/reference_markers.fasta -out GCA_019310565.1_ASM1931056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:32:58,195] [INFO] Task succeeded: Blastn
[2023-06-28 06:32:58,199] [INFO] Selected 20 target genomes.
[2023-06-28 06:32:58,199] [INFO] Target genome list was writen to GCA_019310565.1_ASM1931056v1_genomic.fna/target_genomes.txt
[2023-06-28 06:32:58,201] [INFO] Task started: fastANI
[2023-06-28 06:32:58,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd8085b-c21d-4a0f-b9a4-f994a3f0a5e6/GCA_019310565.1_ASM1931056v1_genomic.fna.gz --refList GCA_019310565.1_ASM1931056v1_genomic.fna/target_genomes.txt --output GCA_019310565.1_ASM1931056v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:33:09,404] [INFO] Task succeeded: fastANI
[2023-06-28 06:33:09,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:33:09,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:33:09,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:33:09,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 06:33:09,406] [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 06:33:09,409] [INFO] DFAST Taxonomy check result was written to GCA_019310565.1_ASM1931056v1_genomic.fna/tc_result.tsv
[2023-06-28 06:33:09,410] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:33:09,410] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:33:09,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference/checkm_data
[2023-06-28 06:33:09,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:33:09,448] [INFO] Task started: CheckM
[2023-06-28 06:33:09,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310565.1_ASM1931056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310565.1_ASM1931056v1_genomic.fna/checkm_input GCA_019310565.1_ASM1931056v1_genomic.fna/checkm_result
[2023-06-28 06:33:36,950] [INFO] Task succeeded: CheckM
[2023-06-28 06:33:36,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.79%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:33:36,973] [INFO] ===== Completeness check finished =====
[2023-06-28 06:33:36,973] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:33:36,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310565.1_ASM1931056v1_genomic.fna/markers.fasta)
[2023-06-28 06:33:36,974] [INFO] Task started: Blastn
[2023-06-28 06:33:36,974] [INFO] Running command: blastn -query GCA_019310565.1_ASM1931056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bbd6001-9e78-4631-99a8-d2a8727745e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310565.1_ASM1931056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:33:37,762] [INFO] Task succeeded: Blastn
[2023-06-28 06:33:37,767] [INFO] Selected 14 target genomes.
[2023-06-28 06:33:37,767] [INFO] Target genome list was writen to GCA_019310565.1_ASM1931056v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:33:37,771] [INFO] Task started: fastANI
[2023-06-28 06:33:37,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd8085b-c21d-4a0f-b9a4-f994a3f0a5e6/GCA_019310565.1_ASM1931056v1_genomic.fna.gz --refList GCA_019310565.1_ASM1931056v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310565.1_ASM1931056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:33:45,997] [INFO] Task succeeded: fastANI
[2023-06-28 06:33:46,005] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:33:46,006] [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_012974475.1	s__JAAXQD01 sp012974475	97.5184	623	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__JAAXQD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002868985.1	s__UBA11574 sp002868985	79.8451	287	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203195.1	s__Desulfatibia_A sp013203195	78.7008	99	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486165.1	s__UBA11574 sp003486165	78.5668	231	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193595.1	s__S5133MH16 sp004193595	78.3183	305	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001751005.1	s__S5133MH16 sp001751005	78.3039	204	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014383215.1	s__Desulfatibia_A vada	78.231	154	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia_A	95.0	99.39	99.39	0.84	0.84	2	-
GCA_014382665.1	s__Desulfatibia profunda	76.8811	166	914	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia	95.0	99.67	99.67	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-28 06:33:46,007] [INFO] GTDB search result was written to GCA_019310565.1_ASM1931056v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:33:46,008] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:33:46,010] [INFO] DFAST_QC result json was written to GCA_019310565.1_ASM1931056v1_genomic.fna/dqc_result.json
[2023-06-28 06:33:46,010] [INFO] DFAST_QC completed!
[2023-06-28 06:33:46,010] [INFO] Total running time: 0h0m57s