[2023-06-08 09:31:55,425] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:31:55,437] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:31:55,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference
[2023-06-08 09:31:57,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:31:57,272] [INFO] Task started: Prodigal
[2023-06-08 09:31:57,273] [INFO] Running command: gunzip -c /var/lib/cwl/stg0acd767d-4a7f-4719-82de-b30ba0b82810/GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:04,106] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:04,107] [INFO] Task started: HMMsearch
[2023-06-08 09:32:04,107] [INFO] Running command: hmmsearch --tblout GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference/reference_markers.hmm GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:04,408] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:04,409] [INFO] Found 6/6 markers.
[2023-06-08 09:32:04,438] [INFO] Query marker FASTA was written to GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:32:04,439] [INFO] Task started: Blastn
[2023-06-08 09:32:04,439] [INFO] Running command: blastn -query GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference/reference_markers.fasta -out GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:05,050] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:05,054] [INFO] Selected 21 target genomes.
[2023-06-08 09:32:05,055] [INFO] Target genome list was writen to GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:32:05,059] [INFO] Task started: fastANI
[2023-06-08 09:32:05,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg0acd767d-4a7f-4719-82de-b30ba0b82810/GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:32:21,166] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:21,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:32:21,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:32:21,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:32:21,171] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:32:21,171] [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
--------------------------------------------------------------------------------
[2023-06-08 09:32:21,173] [INFO] DFAST Taxonomy check result was written to GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:32:21,174] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:32:21,174] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:32:21,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference/checkm_data
[2023-06-08 09:32:21,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:32:21,208] [INFO] Task started: CheckM
[2023-06-08 09:32:21,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:32:46,968] [INFO] Task succeeded: CheckM
[2023-06-08 09:32:46,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:32:46,992] [INFO] ===== Completeness check finished =====
[2023-06-08 09:32:46,993] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:32:46,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:32:46,994] [INFO] Task started: Blastn
[2023-06-08 09:32:46,994] [INFO] Running command: blastn -query GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81244ca5-52ef-436c-a91d-d28132dc53f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:47,857] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:47,869] [INFO] Selected 19 target genomes.
[2023-06-08 09:32:47,869] [INFO] Target genome list was writen to GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:32:47,879] [INFO] Task started: fastANI
[2023-06-08 09:32:47,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg0acd767d-4a7f-4719-82de-b30ba0b82810/GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:32:58,791] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:58,799] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:32:58,800] [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_004554395.1	s__UBA4248 sp004554395	99.3198	632	668	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA4248;f__UBA4248;g__UBA4248	95.0	98.99	98.89	0.91	0.89	4	conclusive
GCA_017441205.1	s__UBA4248 sp017441205	76.8372	56	668	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA4248;f__UBA4248;g__UBA4248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555665.1	s__UBA4248 sp017555665	76.4868	58	668	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA4248;f__UBA4248;g__UBA4248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395385.1	s__UBA4248 sp002395385	76.3761	56	668	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA4248;f__UBA4248;g__UBA4248	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:32:58,801] [INFO] GTDB search result was written to GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:32:58,802] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:32:58,804] [INFO] DFAST_QC result json was written to GCA_945483765.1_SRR7188235_bin.23_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:32:58,804] [INFO] DFAST_QC completed!
[2023-06-08 09:32:58,804] [INFO] Total running time: 0h1m3s