[2023-06-08 14:28:30,525] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:30,527] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:30,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference
[2023-06-08 14:28:33,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:33,210] [INFO] Task started: Prodigal
[2023-06-08 14:28:33,210] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9770c4c-cf0e-45dc-827d-586a627939cb/GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna.gz | prodigal -d GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/cds.fna -a GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:34,865] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:34,866] [INFO] Task started: HMMsearch
[2023-06-08 14:28:34,866] [INFO] Running command: hmmsearch --tblout GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference/reference_markers.hmm GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:35,106] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:35,107] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9770c4c-cf0e-45dc-827d-586a627939cb/GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna.gz]
[2023-06-08 14:28:35,127] [INFO] Query marker FASTA was written to GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/markers.fasta
[2023-06-08 14:28:35,127] [INFO] Task started: Blastn
[2023-06-08 14:28:35,127] [INFO] Running command: blastn -query GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/markers.fasta -db /var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference/reference_markers.fasta -out GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:36,911] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:36,926] [INFO] Selected 21 target genomes.
[2023-06-08 14:28:36,926] [INFO] Target genome list was writen to GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/target_genomes.txt
[2023-06-08 14:28:36,929] [INFO] Task started: fastANI
[2023-06-08 14:28:36,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9770c4c-cf0e-45dc-827d-586a627939cb/GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna.gz --refList GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/target_genomes.txt --output GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:46,258] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:46,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:46,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:46,261] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:46,262] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:28:46,262] [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
--------------------------------------------------------------------------------
[2023-06-08 14:28:46,264] [INFO] DFAST Taxonomy check result was written to GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/tc_result.tsv
[2023-06-08 14:28:46,265] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:46,266] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:46,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference/checkm_data
[2023-06-08 14:28:46,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:46,294] [INFO] Task started: CheckM
[2023-06-08 14:28:46,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/checkm_input GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/checkm_result
[2023-06-08 14:28:59,883] [INFO] Task succeeded: CheckM
[2023-06-08 14:28:59,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:28:59,900] [INFO] ===== Completeness check finished =====
[2023-06-08 14:28:59,900] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:28:59,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/markers.fasta)
[2023-06-08 14:28:59,900] [INFO] Task started: Blastn
[2023-06-08 14:28:59,900] [INFO] Running command: blastn -query GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/markers.fasta -db /var/lib/cwl/stg927c23a7-e32b-4fce-badf-a5c60b0229dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:29:00,670] [INFO] Task succeeded: Blastn
[2023-06-08 14:29:00,673] [INFO] Selected 18 target genomes.
[2023-06-08 14:29:00,674] [INFO] Target genome list was writen to GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:29:00,680] [INFO] Task started: fastANI
[2023-06-08 14:29:00,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9770c4c-cf0e-45dc-827d-586a627939cb/GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna.gz --refList GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/target_genomes_gtdb.txt --output GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:29:06,662] [INFO] Task succeeded: fastANI
[2023-06-08 14:29:06,667] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:29:06,667] [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_902766085.1	s__CAG-793 sp902766085	100.0	281	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000433915.1	s__CAG-793 sp000433915	76.9797	58	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	98.87	98.80	0.92	0.89	3	-
GCA_017510825.1	s__CAG-793 sp017510825	76.5829	60	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:29:06,669] [INFO] GTDB search result was written to GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/result_gtdb.tsv
[2023-06-08 14:29:06,670] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:29:06,672] [INFO] DFAST_QC result json was written to GCA_902766085.1_Rumen_uncultured_genome_RUG11129_genomic.fna/dqc_result.json
[2023-06-08 14:29:06,673] [INFO] DFAST_QC completed!
[2023-06-08 14:29:06,673] [INFO] Total running time: 0h0m36s