[2023-06-28 17:15:31,601] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:15:31,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:15:31,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference
[2023-06-28 17:15:33,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:15:33,380] [INFO] Task started: Prodigal
[2023-06-28 17:15:33,380] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9f301d6-eec5-48e8-ac33-601753b3c1d6/GCA_944324495.1_BRZ_AT_bin62_genomic.fna.gz | prodigal -d GCA_944324495.1_BRZ_AT_bin62_genomic.fna/cds.fna -a GCA_944324495.1_BRZ_AT_bin62_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:15:36,915] [INFO] Task succeeded: Prodigal
[2023-06-28 17:15:36,915] [INFO] Task started: HMMsearch
[2023-06-28 17:15:36,915] [INFO] Running command: hmmsearch --tblout GCA_944324495.1_BRZ_AT_bin62_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference/reference_markers.hmm GCA_944324495.1_BRZ_AT_bin62_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:15:37,111] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:15:37,112] [INFO] Found 6/6 markers.
[2023-06-28 17:15:37,137] [INFO] Query marker FASTA was written to GCA_944324495.1_BRZ_AT_bin62_genomic.fna/markers.fasta
[2023-06-28 17:15:37,137] [INFO] Task started: Blastn
[2023-06-28 17:15:37,137] [INFO] Running command: blastn -query GCA_944324495.1_BRZ_AT_bin62_genomic.fna/markers.fasta -db /var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference/reference_markers.fasta -out GCA_944324495.1_BRZ_AT_bin62_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:15:37,653] [INFO] Task succeeded: Blastn
[2023-06-28 17:15:37,659] [INFO] Selected 17 target genomes.
[2023-06-28 17:15:37,659] [INFO] Target genome list was writen to GCA_944324495.1_BRZ_AT_bin62_genomic.fna/target_genomes.txt
[2023-06-28 17:15:37,660] [INFO] Task started: fastANI
[2023-06-28 17:15:37,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f301d6-eec5-48e8-ac33-601753b3c1d6/GCA_944324495.1_BRZ_AT_bin62_genomic.fna.gz --refList GCA_944324495.1_BRZ_AT_bin62_genomic.fna/target_genomes.txt --output GCA_944324495.1_BRZ_AT_bin62_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:15:42,755] [INFO] Task succeeded: fastANI
[2023-06-28 17:15:42,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:15:42,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:15:42,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:15:42,758] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:15:42,758] [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
--------------------------------------------------------------------------------
[2023-06-28 17:15:42,759] [INFO] DFAST Taxonomy check result was written to GCA_944324495.1_BRZ_AT_bin62_genomic.fna/tc_result.tsv
[2023-06-28 17:15:42,760] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:15:42,760] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:15:42,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference/checkm_data
[2023-06-28 17:15:42,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:15:42,789] [INFO] Task started: CheckM
[2023-06-28 17:15:42,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324495.1_BRZ_AT_bin62_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324495.1_BRZ_AT_bin62_genomic.fna/checkm_input GCA_944324495.1_BRZ_AT_bin62_genomic.fna/checkm_result
[2023-06-28 17:15:59,091] [INFO] Task succeeded: CheckM
[2023-06-28 17:15:59,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:15:59,109] [INFO] ===== Completeness check finished =====
[2023-06-28 17:15:59,109] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:15:59,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324495.1_BRZ_AT_bin62_genomic.fna/markers.fasta)
[2023-06-28 17:15:59,111] [INFO] Task started: Blastn
[2023-06-28 17:15:59,111] [INFO] Running command: blastn -query GCA_944324495.1_BRZ_AT_bin62_genomic.fna/markers.fasta -db /var/lib/cwl/stg70d014c6-1bcf-4835-8246-e092c7b32f6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324495.1_BRZ_AT_bin62_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:16:00,155] [INFO] Task succeeded: Blastn
[2023-06-28 17:16:00,158] [INFO] Selected 17 target genomes.
[2023-06-28 17:16:00,158] [INFO] Target genome list was writen to GCA_944324495.1_BRZ_AT_bin62_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:16:00,165] [INFO] Task started: fastANI
[2023-06-28 17:16:00,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f301d6-eec5-48e8-ac33-601753b3c1d6/GCA_944324495.1_BRZ_AT_bin62_genomic.fna.gz --refList GCA_944324495.1_BRZ_AT_bin62_genomic.fna/target_genomes_gtdb.txt --output GCA_944324495.1_BRZ_AT_bin62_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:16:06,728] [INFO] Task succeeded: fastANI
[2023-06-28 17:16:06,732] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:16:06,732] [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_019116905.1	s__Mucispirillum faecigallinarum	80.6406	427	780	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Mucispirillaceae;g__Mucispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586745.1	s__Mucispirillum sp910586745	80.6298	407	780	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Mucispirillaceae;g__Mucispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000487995.1	s__Mucispirillum schaedleri	80.323	457	780	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Mucispirillaceae;g__Mucispirillum	95.0	99.51	99.14	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-28 17:16:06,734] [INFO] GTDB search result was written to GCA_944324495.1_BRZ_AT_bin62_genomic.fna/result_gtdb.tsv
[2023-06-28 17:16:06,734] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:16:06,736] [INFO] DFAST_QC result json was written to GCA_944324495.1_BRZ_AT_bin62_genomic.fna/dqc_result.json
[2023-06-28 17:16:06,737] [INFO] DFAST_QC completed!
[2023-06-28 17:16:06,737] [INFO] Total running time: 0h0m35s