[2023-06-13 10:22:13,334] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:22:13,336] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:22:13,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference
[2023-06-13 10:22:14,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:22:14,546] [INFO] Task started: Prodigal
[2023-06-13 10:22:14,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg617bf664-1f6c-4190-85dd-d0536734b1b5/GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna.gz | prodigal -d GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/cds.fna -a GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:22:19,653] [INFO] Task succeeded: Prodigal
[2023-06-13 10:22:19,653] [INFO] Task started: HMMsearch
[2023-06-13 10:22:19,654] [INFO] Running command: hmmsearch --tblout GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference/reference_markers.hmm GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:22:19,877] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:22:19,878] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg617bf664-1f6c-4190-85dd-d0536734b1b5/GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna.gz]
[2023-06-13 10:22:19,906] [INFO] Query marker FASTA was written to GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/markers.fasta
[2023-06-13 10:22:19,906] [INFO] Task started: Blastn
[2023-06-13 10:22:19,906] [INFO] Running command: blastn -query GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference/reference_markers.fasta -out GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:22:20,520] [INFO] Task succeeded: Blastn
[2023-06-13 10:22:20,525] [INFO] Selected 28 target genomes.
[2023-06-13 10:22:20,526] [INFO] Target genome list was writen to GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/target_genomes.txt
[2023-06-13 10:22:20,533] [INFO] Task started: fastANI
[2023-06-13 10:22:20,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg617bf664-1f6c-4190-85dd-d0536734b1b5/GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna.gz --refList GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/target_genomes.txt --output GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:22:37,678] [INFO] Task succeeded: fastANI
[2023-06-13 10:22:37,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:22:37,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:22:37,681] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:22:37,682] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:22:37,682] [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 10:22:37,684] [INFO] DFAST Taxonomy check result was written to GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/tc_result.tsv
[2023-06-13 10:22:37,685] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:22:37,686] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:22:37,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference/checkm_data
[2023-06-13 10:22:37,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:22:37,718] [INFO] Task started: CheckM
[2023-06-13 10:22:37,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/checkm_input GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/checkm_result
[2023-06-13 10:23:00,526] [INFO] Task succeeded: CheckM
[2023-06-13 10:23:00,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.79%
Contamintation: 2.31%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 10:23:00,567] [INFO] ===== Completeness check finished =====
[2023-06-13 10:23:00,568] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:23:00,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/markers.fasta)
[2023-06-13 10:23:00,569] [INFO] Task started: Blastn
[2023-06-13 10:23:00,569] [INFO] Running command: blastn -query GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dd0c72d-f8ba-418f-9fa9-a8496fa79fcd/dqc_reference/reference_markers_gtdb.fasta -out GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:23:01,545] [INFO] Task succeeded: Blastn
[2023-06-13 10:23:01,550] [INFO] Selected 23 target genomes.
[2023-06-13 10:23:01,550] [INFO] Target genome list was writen to GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:23:01,566] [INFO] Task started: fastANI
[2023-06-13 10:23:01,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg617bf664-1f6c-4190-85dd-d0536734b1b5/GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna.gz --refList GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:23:17,826] [INFO] Task succeeded: fastANI
[2023-06-13 10:23:17,831] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:23:17,831] [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_011087745.1	s__JAALLB01 sp011087745	78.389	153	608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAALLB01	95.0	99.84	99.84	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-13 10:23:17,833] [INFO] GTDB search result was written to GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:23:17,834] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:23:17,836] [INFO] DFAST_QC result json was written to GCA_938030595.1_R3_Bin_Bin_49_1_genomic.fna/dqc_result.json
[2023-06-13 10:23:17,836] [INFO] DFAST_QC completed!
[2023-06-13 10:23:17,836] [INFO] Total running time: 0h1m5s