[2023-06-28 14:45:11,296] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:45:11,298] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:45:11,299] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference
[2023-06-28 14:45:12,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:45:12,471] [INFO] Task started: Prodigal
[2023-06-28 14:45:12,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg50e25e0e-961f-4ec8-9649-2061864cfe51/GCA_017996595.1_ASM1799659v1_genomic.fna.gz | prodigal -d GCA_017996595.1_ASM1799659v1_genomic.fna/cds.fna -a GCA_017996595.1_ASM1799659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:45:15,505] [INFO] Task succeeded: Prodigal
[2023-06-28 14:45:15,506] [INFO] Task started: HMMsearch
[2023-06-28 14:45:15,506] [INFO] Running command: hmmsearch --tblout GCA_017996595.1_ASM1799659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference/reference_markers.hmm GCA_017996595.1_ASM1799659v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:45:15,666] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:45:15,668] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg50e25e0e-961f-4ec8-9649-2061864cfe51/GCA_017996595.1_ASM1799659v1_genomic.fna.gz]
[2023-06-28 14:45:15,688] [INFO] Query marker FASTA was written to GCA_017996595.1_ASM1799659v1_genomic.fna/markers.fasta
[2023-06-28 14:45:15,688] [INFO] Task started: Blastn
[2023-06-28 14:45:15,689] [INFO] Running command: blastn -query GCA_017996595.1_ASM1799659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference/reference_markers.fasta -out GCA_017996595.1_ASM1799659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:45:16,170] [INFO] Task succeeded: Blastn
[2023-06-28 14:45:16,174] [INFO] Selected 5 target genomes.
[2023-06-28 14:45:16,174] [INFO] Target genome list was writen to GCA_017996595.1_ASM1799659v1_genomic.fna/target_genomes.txt
[2023-06-28 14:45:16,175] [INFO] Task started: fastANI
[2023-06-28 14:45:16,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg50e25e0e-961f-4ec8-9649-2061864cfe51/GCA_017996595.1_ASM1799659v1_genomic.fna.gz --refList GCA_017996595.1_ASM1799659v1_genomic.fna/target_genomes.txt --output GCA_017996595.1_ASM1799659v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:45:19,628] [INFO] Task succeeded: fastANI
[2023-06-28 14:45:19,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:45:19,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:45:19,630] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:45:19,630] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:45:19,631] [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 14:45:19,634] [INFO] DFAST Taxonomy check result was written to GCA_017996595.1_ASM1799659v1_genomic.fna/tc_result.tsv
[2023-06-28 14:45:19,636] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:45:19,637] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:45:19,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference/checkm_data
[2023-06-28 14:45:19,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:45:19,657] [INFO] Task started: CheckM
[2023-06-28 14:45:19,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017996595.1_ASM1799659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017996595.1_ASM1799659v1_genomic.fna/checkm_input GCA_017996595.1_ASM1799659v1_genomic.fna/checkm_result
[2023-06-28 14:45:35,503] [INFO] Task succeeded: CheckM
[2023-06-28 14:45:35,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 34.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:45:35,525] [INFO] ===== Completeness check finished =====
[2023-06-28 14:45:35,525] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:45:35,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017996595.1_ASM1799659v1_genomic.fna/markers.fasta)
[2023-06-28 14:45:35,526] [INFO] Task started: Blastn
[2023-06-28 14:45:35,526] [INFO] Running command: blastn -query GCA_017996595.1_ASM1799659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4de8afa-d729-494a-b5bf-c8b4853fd2ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_017996595.1_ASM1799659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:45:35,957] [INFO] Task succeeded: Blastn
[2023-06-28 14:45:35,962] [INFO] Selected 9 target genomes.
[2023-06-28 14:45:35,962] [INFO] Target genome list was writen to GCA_017996595.1_ASM1799659v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:45:35,964] [INFO] Task started: fastANI
[2023-06-28 14:45:35,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg50e25e0e-961f-4ec8-9649-2061864cfe51/GCA_017996595.1_ASM1799659v1_genomic.fna.gz --refList GCA_017996595.1_ASM1799659v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017996595.1_ASM1799659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:45:39,269] [INFO] Task succeeded: fastANI
[2023-06-28 14:45:39,273] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:45:39,274] [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_017996595.1	s__Cloacimonas sp017996595	100.0	341	347	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Cloacimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428685.1	s__Cloacimonas sp002428685	77.2252	76	347	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Cloacimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840645.1	s__Cloacimonas sp002840645	76.8137	61	347	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Cloacimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:45:39,275] [INFO] GTDB search result was written to GCA_017996595.1_ASM1799659v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:45:39,276] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:45:39,279] [INFO] DFAST_QC result json was written to GCA_017996595.1_ASM1799659v1_genomic.fna/dqc_result.json
[2023-06-28 14:45:39,279] [INFO] DFAST_QC completed!
[2023-06-28 14:45:39,280] [INFO] Total running time: 0h0m28s