[2023-06-13 01:24:33,577] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:24:33,581] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:24:33,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference
[2023-06-13 01:24:34,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:24:34,976] [INFO] Task started: Prodigal
[2023-06-13 01:24:34,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fa5a210-e194-45d4-aa62-0cfdc38aa4eb/GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:24:41,869] [INFO] Task succeeded: Prodigal
[2023-06-13 01:24:41,870] [INFO] Task started: HMMsearch
[2023-06-13 01:24:41,870] [INFO] Running command: hmmsearch --tblout GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference/reference_markers.hmm GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:24:42,095] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:24:42,096] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0fa5a210-e194-45d4-aa62-0cfdc38aa4eb/GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 01:24:42,119] [INFO] Query marker FASTA was written to GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 01:24:42,119] [INFO] Task started: Blastn
[2023-06-13 01:24:42,120] [INFO] Running command: blastn -query GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference/reference_markers.fasta -out GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:24:42,684] [INFO] Task succeeded: Blastn
[2023-06-13 01:24:42,688] [INFO] Selected 16 target genomes.
[2023-06-13 01:24:42,688] [INFO] Target genome list was writen to GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 01:24:42,689] [INFO] Task started: fastANI
[2023-06-13 01:24:42,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fa5a210-e194-45d4-aa62-0cfdc38aa4eb/GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:24:52,620] [INFO] Task succeeded: fastANI
[2023-06-13 01:24:52,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:24:52,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:24:52,626] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 01:24:52,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 01:24:52,627] [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
Faecalibaculum rodentium	strain=ALO17	GCA_001564455.1	1702221	1702221	type	True	97.8544	695	766	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 01:24:52,629] [INFO] DFAST Taxonomy check result was written to GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 01:24:52,630] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:24:52,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:24:52,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference/checkm_data
[2023-06-13 01:24:52,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:24:52,663] [INFO] Task started: CheckM
[2023-06-13 01:24:52,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 01:25:20,364] [INFO] Task succeeded: CheckM
[2023-06-13 01:25:20,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:25:20,392] [INFO] ===== Completeness check finished =====
[2023-06-13 01:25:20,392] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:25:20,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 01:25:20,393] [INFO] Task started: Blastn
[2023-06-13 01:25:20,393] [INFO] Running command: blastn -query GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg38cae5f3-f0d5-42a4-814e-3aaec45ecfa0/dqc_reference/reference_markers_gtdb.fasta -out GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:25:21,133] [INFO] Task succeeded: Blastn
[2023-06-13 01:25:21,136] [INFO] Selected 20 target genomes.
[2023-06-13 01:25:21,136] [INFO] Target genome list was writen to GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:25:21,140] [INFO] Task started: fastANI
[2023-06-13 01:25:21,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fa5a210-e194-45d4-aa62-0cfdc38aa4eb/GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:25:31,652] [INFO] Task succeeded: fastANI
[2023-06-13 01:25:31,657] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 01:25:31,657] [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
GCF_001564455.1	s__Faecalibaculum rodentium	97.8544	695	766	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum	95.0	97.78	97.75	0.92	0.90	4	conclusive
GCA_910588395.1	s__Faecalibaculum sp910588395	82.0286	458	766	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:25:31,659] [INFO] GTDB search result was written to GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 01:25:31,660] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:25:31,663] [INFO] DFAST_QC result json was written to GCA_947073665.1_SRR12464005_bin.23_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 01:25:31,664] [INFO] DFAST_QC completed!
[2023-06-13 01:25:31,664] [INFO] Total running time: 0h0m58s