[2023-06-08 09:31:51,318] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:31:51,321] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:31:51,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference
[2023-06-08 09:31:54,621] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:31:54,623] [INFO] Task started: Prodigal
[2023-06-08 09:31:54,624] [INFO] Running command: gunzip -c /var/lib/cwl/stge3672ac3-9ecf-493b-8d20-1b215b2e74bb/GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:05,377] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:05,378] [INFO] Task started: HMMsearch
[2023-06-08 09:32:05,378] [INFO] Running command: hmmsearch --tblout GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference/reference_markers.hmm GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:05,621] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:05,622] [INFO] Found 6/6 markers.
[2023-06-08 09:32:05,645] [INFO] Query marker FASTA was written to GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:32:05,645] [INFO] Task started: Blastn
[2023-06-08 09:32:05,645] [INFO] Running command: blastn -query GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference/reference_markers.fasta -out GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:06,209] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:06,213] [INFO] Selected 33 target genomes.
[2023-06-08 09:32:06,214] [INFO] Target genome list was writen to GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:32:06,221] [INFO] Task started: fastANI
[2023-06-08 09:32:06,221] [INFO] Running command: fastANI --query /var/lib/cwl/stge3672ac3-9ecf-493b-8d20-1b215b2e74bb/GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:32:25,282] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:25,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:32:25,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:32:25,285] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:32:25,286] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:32:25,286] [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 09:32:25,288] [INFO] DFAST Taxonomy check result was written to GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:32:25,289] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:32:25,289] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:32:25,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference/checkm_data
[2023-06-08 09:32:25,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:32:25,318] [INFO] Task started: CheckM
[2023-06-08 09:32:25,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:32:59,942] [INFO] Task succeeded: CheckM
[2023-06-08 09:32:59,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:32:59,962] [INFO] ===== Completeness check finished =====
[2023-06-08 09:32:59,963] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:32:59,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:32:59,964] [INFO] Task started: Blastn
[2023-06-08 09:32:59,964] [INFO] Running command: blastn -query GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg919be3c4-0ee4-4ed0-8aa7-bad6812055fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:33:00,733] [INFO] Task succeeded: Blastn
[2023-06-08 09:33:00,740] [INFO] Selected 34 target genomes.
[2023-06-08 09:33:00,740] [INFO] Target genome list was writen to GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:33:00,783] [INFO] Task started: fastANI
[2023-06-08 09:33:00,783] [INFO] Running command: fastANI --query /var/lib/cwl/stge3672ac3-9ecf-493b-8d20-1b215b2e74bb/GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:33:13,589] [INFO] Task succeeded: fastANI
[2023-06-08 09:33:13,597] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:33:13,597] [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_018064985.1	s__RF16 sp018064985	78.3888	138	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321775.1	s__RF16 sp900321775	77.2964	56	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.90	95.79	0.79	0.59	13	-
GCA_002373505.1	s__RF16 sp002373505	75.9553	54	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.32	96.25	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-08 09:33:13,602] [INFO] GTDB search result was written to GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:33:13,602] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:33:13,621] [INFO] DFAST_QC result json was written to GCA_945923565.1_SRR11489748_bin.46_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:33:13,621] [INFO] DFAST_QC completed!
[2023-06-08 09:33:13,621] [INFO] Total running time: 0h1m22s