[2023-06-13 05:49:43,261] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:49:43,279] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:49:43,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference
[2023-06-13 05:49:44,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:49:44,526] [INFO] Task started: Prodigal
[2023-06-13 05:49:44,526] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd31811c-0421-43fb-873c-91648410f0f0/GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna.gz | prodigal -d GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/cds.fna -a GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:49:48,956] [INFO] Task succeeded: Prodigal
[2023-06-13 05:49:48,956] [INFO] Task started: HMMsearch
[2023-06-13 05:49:48,956] [INFO] Running command: hmmsearch --tblout GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference/reference_markers.hmm GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:49:49,090] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:49:49,091] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgbd31811c-0421-43fb-873c-91648410f0f0/GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna.gz]
[2023-06-13 05:49:49,109] [INFO] Query marker FASTA was written to GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/markers.fasta
[2023-06-13 05:49:49,110] [INFO] Task started: Blastn
[2023-06-13 05:49:49,110] [INFO] Running command: blastn -query GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference/reference_markers.fasta -out GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:49:49,602] [INFO] Task succeeded: Blastn
[2023-06-13 05:49:49,609] [INFO] Selected 10 target genomes.
[2023-06-13 05:49:49,609] [INFO] Target genome list was writen to GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/target_genomes.txt
[2023-06-13 05:49:49,612] [INFO] Task started: fastANI
[2023-06-13 05:49:49,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd31811c-0421-43fb-873c-91648410f0f0/GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna.gz --refList GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/target_genomes.txt --output GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:49:57,001] [INFO] Task succeeded: fastANI
[2023-06-13 05:49:57,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:49:57,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:49:57,003] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:49:57,003] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:49:57,003] [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
--------------------------------------------------------------------------------
[2023-06-13 05:49:57,005] [INFO] DFAST Taxonomy check result was written to GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/tc_result.tsv
[2023-06-13 05:49:57,006] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:49:57,006] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:49:57,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference/checkm_data
[2023-06-13 05:49:57,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:49:57,055] [INFO] Task started: CheckM
[2023-06-13 05:49:57,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/checkm_input GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/checkm_result
[2023-06-13 05:50:16,165] [INFO] Task succeeded: CheckM
[2023-06-13 05:50:16,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:50:16,188] [INFO] ===== Completeness check finished =====
[2023-06-13 05:50:16,189] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:50:16,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/markers.fasta)
[2023-06-13 05:50:16,189] [INFO] Task started: Blastn
[2023-06-13 05:50:16,189] [INFO] Running command: blastn -query GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8691a6f2-f65f-4aea-b0a5-b86963d4470e/dqc_reference/reference_markers_gtdb.fasta -out GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:16,714] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:16,720] [INFO] Selected 9 target genomes.
[2023-06-13 05:50:16,720] [INFO] Target genome list was writen to GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:50:16,735] [INFO] Task started: fastANI
[2023-06-13 05:50:16,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd31811c-0421-43fb-873c-91648410f0f0/GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna.gz --refList GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:50:23,931] [INFO] Task succeeded: fastANI
[2023-06-13 05:50:23,938] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:50:23,938] [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_905479125.1	s__UBA830 sp905479125	99.1562	399	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	conclusive
GCA_905181725.1	s__UBA830 sp905181725	82.8319	369	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471575.1	s__UBA830 sp002471575	77.1936	147	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_009377375.1	s__WHUE01 sp009377375	76.5129	75	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:50:23,943] [INFO] GTDB search result was written to GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:50:23,945] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:50:23,963] [INFO] DFAST_QC result json was written to GCA_938082385.1_S2_Bin_METABAT_130_1_genomic.fna/dqc_result.json
[2023-06-13 05:50:23,963] [INFO] DFAST_QC completed!
[2023-06-13 05:50:23,963] [INFO] Total running time: 0h0m41s