[2023-06-06 00:02:20,827] [INFO] DFAST_QC pipeline started.
[2023-06-06 00:02:20,829] [INFO] DFAST_QC version: 0.5.7
[2023-06-06 00:02:20,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference
[2023-06-06 00:02:22,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-06 00:02:22,621] [INFO] Task started: Prodigal
[2023-06-06 00:02:22,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg51e416de-ca87-4c17-b2d1-f31c99dac64b/GCA_902727985.1_HLG_WM_MAG_07_genomic.fna.gz | prodigal -d GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/cds.fna -a GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-06 00:02:30,311] [INFO] Task succeeded: Prodigal
[2023-06-06 00:02:30,311] [INFO] Task started: HMMsearch
[2023-06-06 00:02:30,311] [INFO] Running command: hmmsearch --tblout GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference/reference_markers.hmm GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/protein.faa > /dev/null
[2023-06-06 00:02:30,536] [INFO] Task succeeded: HMMsearch
[2023-06-06 00:02:30,537] [INFO] Found 6/6 markers.
[2023-06-06 00:02:30,567] [INFO] Query marker FASTA was written to GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/markers.fasta
[2023-06-06 00:02:30,567] [INFO] Task started: Blastn
[2023-06-06 00:02:30,567] [INFO] Running command: blastn -query GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/markers.fasta -db /var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference/reference_markers.fasta -out GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:02:31,200] [INFO] Task succeeded: Blastn
[2023-06-06 00:02:31,205] [INFO] Selected 32 target genomes.
[2023-06-06 00:02:31,205] [INFO] Target genome list was writen to GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/target_genomes.txt
[2023-06-06 00:02:31,211] [INFO] Task started: fastANI
[2023-06-06 00:02:31,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg51e416de-ca87-4c17-b2d1-f31c99dac64b/GCA_902727985.1_HLG_WM_MAG_07_genomic.fna.gz --refList GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/target_genomes.txt --output GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/fastani_result.tsv --threads 1
[2023-06-06 00:02:51,919] [INFO] Task succeeded: fastANI
[2023-06-06 00:02:51,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-06 00:02:51,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-06 00:02:51,922] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-06 00:02:51,922] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-06 00:02:51,922] [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
--------------------------------------------------------------------------------
[2023-06-06 00:02:51,924] [INFO] DFAST Taxonomy check result was written to GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/tc_result.tsv
[2023-06-06 00:02:51,925] [INFO] ===== Taxonomy check completed =====
[2023-06-06 00:02:51,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-06 00:02:51,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference/checkm_data
[2023-06-06 00:02:51,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-06 00:02:51,992] [INFO] Task started: CheckM
[2023-06-06 00:02:51,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/checkm_input GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/checkm_result
[2023-06-06 00:03:20,707] [INFO] Task succeeded: CheckM
[2023-06-06 00:03:20,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-06 00:03:20,728] [INFO] ===== Completeness check finished =====
[2023-06-06 00:03:20,728] [INFO] ===== Start GTDB Search =====
[2023-06-06 00:03:20,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/markers.fasta)
[2023-06-06 00:03:20,729] [INFO] Task started: Blastn
[2023-06-06 00:03:20,729] [INFO] Running command: blastn -query GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/markers.fasta -db /var/lib/cwl/stg39fe625d-5170-46fd-b27d-d1f4a43ad582/dqc_reference/reference_markers_gtdb.fasta -out GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:03:21,872] [INFO] Task succeeded: Blastn
[2023-06-06 00:03:21,925] [INFO] Selected 26 target genomes.
[2023-06-06 00:03:21,928] [INFO] Target genome list was writen to GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/target_genomes_gtdb.txt
[2023-06-06 00:03:22,356] [INFO] Task started: fastANI
[2023-06-06 00:03:22,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg51e416de-ca87-4c17-b2d1-f31c99dac64b/GCA_902727985.1_HLG_WM_MAG_07_genomic.fna.gz --refList GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/target_genomes_gtdb.txt --output GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-06 00:03:36,073] [INFO] Task succeeded: fastANI
[2023-06-06 00:03:36,078] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-06 00:03:36,078] [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_902727985.1	s__HyVt-477 sp902727985	100.0	1092	1098	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__HyVt-477	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-06 00:03:36,080] [INFO] GTDB search result was written to GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/result_gtdb.tsv
[2023-06-06 00:03:36,081] [INFO] ===== GTDB Search completed =====
[2023-06-06 00:03:36,083] [INFO] DFAST_QC result json was written to GCA_902727985.1_HLG_WM_MAG_07_genomic.fna/dqc_result.json
[2023-06-06 00:03:36,084] [INFO] DFAST_QC completed!
[2023-06-06 00:03:36,084] [INFO] Total running time: 0h1m15s