[2023-06-13 23:34:34,236] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:34:34,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:34:34,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference
[2023-06-13 23:34:36,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:34:36,198] [INFO] Task started: Prodigal
[2023-06-13 23:34:36,199] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3ddfee4-0f98-42bf-a74a-844d8ae5871f/GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna.gz | prodigal -d GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/cds.fna -a GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:34:50,795] [INFO] Task succeeded: Prodigal
[2023-06-13 23:34:50,796] [INFO] Task started: HMMsearch
[2023-06-13 23:34:50,796] [INFO] Running command: hmmsearch --tblout GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference/reference_markers.hmm GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:34:51,028] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:34:51,029] [INFO] Found 6/6 markers.
[2023-06-13 23:34:51,072] [INFO] Query marker FASTA was written to GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/markers.fasta
[2023-06-13 23:34:51,073] [INFO] Task started: Blastn
[2023-06-13 23:34:51,073] [INFO] Running command: blastn -query GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference/reference_markers.fasta -out GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:34:51,662] [INFO] Task succeeded: Blastn
[2023-06-13 23:34:51,667] [INFO] Selected 28 target genomes.
[2023-06-13 23:34:51,668] [INFO] Target genome list was writen to GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/target_genomes.txt
[2023-06-13 23:34:51,674] [INFO] Task started: fastANI
[2023-06-13 23:34:51,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ddfee4-0f98-42bf-a74a-844d8ae5871f/GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna.gz --refList GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/target_genomes.txt --output GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:35:09,228] [INFO] Task succeeded: fastANI
[2023-06-13 23:35:09,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:35:09,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:35:09,234] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:35:09,234] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 23:35:09,234] [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 23:35:09,238] [INFO] DFAST Taxonomy check result was written to GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/tc_result.tsv
[2023-06-13 23:35:09,238] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:35:09,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:35:09,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference/checkm_data
[2023-06-13 23:35:09,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:35:09,278] [INFO] Task started: CheckM
[2023-06-13 23:35:09,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/checkm_input GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/checkm_result
[2023-06-13 23:35:54,983] [INFO] Task succeeded: CheckM
[2023-06-13 23:35:54,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:35:55,006] [INFO] ===== Completeness check finished =====
[2023-06-13 23:35:55,006] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:35:55,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/markers.fasta)
[2023-06-13 23:35:55,007] [INFO] Task started: Blastn
[2023-06-13 23:35:55,007] [INFO] Running command: blastn -query GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2029ddd-8212-4b97-9026-19a8f73bc09f/dqc_reference/reference_markers_gtdb.fasta -out GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:35:55,768] [INFO] Task succeeded: Blastn
[2023-06-13 23:35:55,773] [INFO] Selected 32 target genomes.
[2023-06-13 23:35:55,774] [INFO] Target genome list was writen to GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:35:55,853] [INFO] Task started: fastANI
[2023-06-13 23:35:55,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ddfee4-0f98-42bf-a74a-844d8ae5871f/GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna.gz --refList GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:36:12,396] [INFO] Task succeeded: fastANI
[2023-06-13 23:36:12,401] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:36:12,401] [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_017859335.1	s__JAAZVD01 sp017859335	78.582	169	761	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__JAAZVD01	95.0	99.32	99.32	0.92	0.92	2	-
GCA_018623785.1	s__JAAZVD01 sp018623785	77.5756	106	761	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__JAAZVD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:36:12,404] [INFO] GTDB search result was written to GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:36:12,404] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:36:12,407] [INFO] DFAST_QC result json was written to GCA_938018055.1_S1_Bin_Bin_34_sub_1_genomic.fna/dqc_result.json
[2023-06-13 23:36:12,407] [INFO] DFAST_QC completed!
[2023-06-13 23:36:12,407] [INFO] Total running time: 0h1m38s