[2023-06-28 12:59:25,398] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:59:25,401] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:59:25,401] [INFO] DQC Reference Directory: /var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference
[2023-06-28 12:59:26,790] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:59:26,791] [INFO] Task started: Prodigal
[2023-06-28 12:59:26,791] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0f50011-cbe0-48e5-ac27-b550b1959d24/GCA_019310585.1_ASM1931058v1_genomic.fna.gz | prodigal -d GCA_019310585.1_ASM1931058v1_genomic.fna/cds.fna -a GCA_019310585.1_ASM1931058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:59:32,968] [INFO] Task succeeded: Prodigal
[2023-06-28 12:59:32,968] [INFO] Task started: HMMsearch
[2023-06-28 12:59:32,968] [INFO] Running command: hmmsearch --tblout GCA_019310585.1_ASM1931058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference/reference_markers.hmm GCA_019310585.1_ASM1931058v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:59:33,249] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:59:33,251] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf0f50011-cbe0-48e5-ac27-b550b1959d24/GCA_019310585.1_ASM1931058v1_genomic.fna.gz]
[2023-06-28 12:59:33,283] [INFO] Query marker FASTA was written to GCA_019310585.1_ASM1931058v1_genomic.fna/markers.fasta
[2023-06-28 12:59:33,284] [INFO] Task started: Blastn
[2023-06-28 12:59:33,284] [INFO] Running command: blastn -query GCA_019310585.1_ASM1931058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference/reference_markers.fasta -out GCA_019310585.1_ASM1931058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:59:33,922] [INFO] Task succeeded: Blastn
[2023-06-28 12:59:33,926] [INFO] Selected 17 target genomes.
[2023-06-28 12:59:33,926] [INFO] Target genome list was writen to GCA_019310585.1_ASM1931058v1_genomic.fna/target_genomes.txt
[2023-06-28 12:59:33,927] [INFO] Task started: fastANI
[2023-06-28 12:59:33,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0f50011-cbe0-48e5-ac27-b550b1959d24/GCA_019310585.1_ASM1931058v1_genomic.fna.gz --refList GCA_019310585.1_ASM1931058v1_genomic.fna/target_genomes.txt --output GCA_019310585.1_ASM1931058v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:59:45,921] [INFO] Task succeeded: fastANI
[2023-06-28 12:59:45,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:59:45,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:59:45,923] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:59:45,924] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:59:45,924] [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 12:59:45,926] [INFO] DFAST Taxonomy check result was written to GCA_019310585.1_ASM1931058v1_genomic.fna/tc_result.tsv
[2023-06-28 12:59:45,926] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:59:45,926] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:59:45,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference/checkm_data
[2023-06-28 12:59:45,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:59:45,960] [INFO] Task started: CheckM
[2023-06-28 12:59:45,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310585.1_ASM1931058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310585.1_ASM1931058v1_genomic.fna/checkm_input GCA_019310585.1_ASM1931058v1_genomic.fna/checkm_result
[2023-06-28 13:00:11,296] [INFO] Task succeeded: CheckM
[2023-06-28 13:00:11,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:00:11,319] [INFO] ===== Completeness check finished =====
[2023-06-28 13:00:11,320] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:00:11,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310585.1_ASM1931058v1_genomic.fna/markers.fasta)
[2023-06-28 13:00:11,321] [INFO] Task started: Blastn
[2023-06-28 13:00:11,321] [INFO] Running command: blastn -query GCA_019310585.1_ASM1931058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefee874-fcc6-414b-a762-67892b5dc0c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310585.1_ASM1931058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:00:12,132] [INFO] Task succeeded: Blastn
[2023-06-28 13:00:12,137] [INFO] Selected 12 target genomes.
[2023-06-28 13:00:12,137] [INFO] Target genome list was writen to GCA_019310585.1_ASM1931058v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:00:12,163] [INFO] Task started: fastANI
[2023-06-28 13:00:12,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0f50011-cbe0-48e5-ac27-b550b1959d24/GCA_019310585.1_ASM1931058v1_genomic.fna.gz --refList GCA_019310585.1_ASM1931058v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310585.1_ASM1931058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:00:20,677] [INFO] Task succeeded: fastANI
[2023-06-28 13:00:20,689] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:00:20,690] [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_004193595.1	s__S5133MH16 sp004193595	88.9163	613	782	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	86.6327	399	782	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868985.1	s__UBA11574 sp002868985	77.3831	154	782	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012974475.1	s__JAAXQD01 sp012974475	77.3826	184	782	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__JAAXQD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203195.1	s__Desulfatibia_A sp013203195	76.9448	89	782	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	76.8159	133	782	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382665.1	s__Desulfatibia profunda	76.7474	131	782	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 13:00:20,692] [INFO] GTDB search result was written to GCA_019310585.1_ASM1931058v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:00:20,692] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:00:20,695] [INFO] DFAST_QC result json was written to GCA_019310585.1_ASM1931058v1_genomic.fna/dqc_result.json
[2023-06-28 13:00:20,695] [INFO] DFAST_QC completed!
[2023-06-28 13:00:20,695] [INFO] Total running time: 0h0m55s