[2023-06-29 08:45:04,368] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:45:04,370] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:45:04,370] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference
[2023-06-29 08:45:05,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:45:05,751] [INFO] Task started: Prodigal
[2023-06-29 08:45:05,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a170798-49c2-4afe-8298-f3e6cbf2a103/GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:45:10,179] [INFO] Task succeeded: Prodigal
[2023-06-29 08:45:10,179] [INFO] Task started: HMMsearch
[2023-06-29 08:45:10,179] [INFO] Running command: hmmsearch --tblout GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference/reference_markers.hmm GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:45:10,427] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:45:10,428] [INFO] Found 6/6 markers.
[2023-06-29 08:45:10,453] [INFO] Query marker FASTA was written to GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 08:45:10,453] [INFO] Task started: Blastn
[2023-06-29 08:45:10,453] [INFO] Running command: blastn -query GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference/reference_markers.fasta -out GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:11,015] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:11,020] [INFO] Selected 21 target genomes.
[2023-06-29 08:45:11,021] [INFO] Target genome list was writen to GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 08:45:11,027] [INFO] Task started: fastANI
[2023-06-29 08:45:11,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a170798-49c2-4afe-8298-f3e6cbf2a103/GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:45:20,636] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:20,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:45:20,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:45:20,639] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:45:20,639] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 08:45:20,639] [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
--------------------------------------------------------------------------------
[2023-06-29 08:45:20,641] [INFO] DFAST Taxonomy check result was written to GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 08:45:20,642] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:45:20,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:45:20,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference/checkm_data
[2023-06-29 08:45:20,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:45:20,678] [INFO] Task started: CheckM
[2023-06-29 08:45:20,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 08:45:41,552] [INFO] Task succeeded: CheckM
[2023-06-29 08:45:41,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:45:41,576] [INFO] ===== Completeness check finished =====
[2023-06-29 08:45:41,577] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:45:41,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 08:45:41,577] [INFO] Task started: Blastn
[2023-06-29 08:45:41,577] [INFO] Running command: blastn -query GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4741f9f-6810-4699-ac14-fa30e5c4bb0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:42,322] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:42,328] [INFO] Selected 32 target genomes.
[2023-06-29 08:45:42,328] [INFO] Target genome list was writen to GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:45:42,347] [INFO] Task started: fastANI
[2023-06-29 08:45:42,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a170798-49c2-4afe-8298-f3e6cbf2a103/GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:45:55,360] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:55,365] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:45:55,365] [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_910579745.1	s__MGBC114079 sp910579745	79.0159	305	735	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__MGBC114079	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:45:55,368] [INFO] GTDB search result was written to GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 08:45:55,368] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:45:55,371] [INFO] DFAST_QC result json was written to GCA_948441255.1_SRR15730552_bin.19_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 08:45:55,371] [INFO] DFAST_QC completed!
[2023-06-29 08:45:55,371] [INFO] Total running time: 0h0m51s