[2023-06-30 14:16:55,675] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:16:55,677] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:16:55,677] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdf611b1-c3f8-4284-8039-f322a15bb1df/dqc_reference
[2023-06-30 14:16:57,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:16:57,737] [INFO] Task started: Prodigal
[2023-06-30 14:16:57,737] [INFO] Running command: gunzip -c /var/lib/cwl/stgc418ff6f-a2ea-4f16-8c2d-176e8f2f6b49/GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna.gz | prodigal -d GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/cds.fna -a GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:17:02,058] [INFO] Task succeeded: Prodigal
[2023-06-30 14:17:02,058] [INFO] Task started: HMMsearch
[2023-06-30 14:17:02,059] [INFO] Running command: hmmsearch --tblout GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdf611b1-c3f8-4284-8039-f322a15bb1df/dqc_reference/reference_markers.hmm GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:17:02,245] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:17:02,246] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc418ff6f-a2ea-4f16-8c2d-176e8f2f6b49/GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna.gz]
[2023-06-30 14:17:02,272] [INFO] Query marker FASTA was written to GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/markers.fasta
[2023-06-30 14:17:02,272] [INFO] Task started: Blastn
[2023-06-30 14:17:02,272] [INFO] Running command: blastn -query GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdf611b1-c3f8-4284-8039-f322a15bb1df/dqc_reference/reference_markers.fasta -out GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:17:02,738] [INFO] Task succeeded: Blastn
[2023-06-30 14:17:02,742] [INFO] Selected 0 target genomes.
[2023-06-30 14:17:02,742] [INFO] Target genome list was writen to GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/target_genomes.txt
[2023-06-30 14:17:02,743] [ERROR] File is empty. [GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/target_genomes.txt]
[2023-06-30 14:17:02,743] [ERROR] Task failed. No target genome found.
[2023-06-30 14:17:02,743] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:17:02,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdf611b1-c3f8-4284-8039-f322a15bb1df/dqc_reference/checkm_data
[2023-06-30 14:17:02,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:17:02,774] [INFO] Task started: CheckM
[2023-06-30 14:17:02,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/checkm_input GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/checkm_result
[2023-06-30 14:17:23,507] [INFO] Task succeeded: CheckM
[2023-06-30 14:17:23,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:17:23,529] [INFO] ===== Completeness check finished =====
[2023-06-30 14:17:23,530] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:17:23,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/markers.fasta)
[2023-06-30 14:17:23,531] [INFO] Task started: Blastn
[2023-06-30 14:17:23,531] [INFO] Running command: blastn -query GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdf611b1-c3f8-4284-8039-f322a15bb1df/dqc_reference/reference_markers_gtdb.fasta -out GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:17:23,997] [INFO] Task succeeded: Blastn
[2023-06-30 14:17:24,001] [INFO] Selected 1 target genomes.
[2023-06-30 14:17:24,001] [INFO] Target genome list was writen to GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:17:24,002] [INFO] Task started: fastANI
[2023-06-30 14:17:24,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgc418ff6f-a2ea-4f16-8c2d-176e8f2f6b49/GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna.gz --refList GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/target_genomes_gtdb.txt --output GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:17:24,853] [INFO] Task succeeded: fastANI
[2023-06-30 14:17:24,856] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:17:24,856] [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
--------------------------------------------------------------------------------
[2023-06-30 14:17:24,860] [INFO] GTDB search result was written to GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/result_gtdb.tsv
[2023-06-30 14:17:24,861] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:17:24,864] [INFO] DFAST_QC result json was written to GCA_903855555.1_freshwater_MAG_---_Ki3-D2_bin-1290_genomic.fna/dqc_result.json
[2023-06-30 14:17:24,865] [INFO] DFAST_QC completed!
[2023-06-30 14:17:24,865] [INFO] Total running time: 0h0m29s