[2023-06-07 21:53:51,362] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:53:51,365] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:53:51,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference
[2023-06-07 21:53:52,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:53:52,563] [INFO] Task started: Prodigal
[2023-06-07 21:53:52,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg10d0047f-889c-4b4a-8544-dd04c6b2d01a/GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna.gz | prodigal -d GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/cds.fna -a GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:53:56,373] [INFO] Task succeeded: Prodigal
[2023-06-07 21:53:56,374] [INFO] Task started: HMMsearch
[2023-06-07 21:53:56,374] [INFO] Running command: hmmsearch --tblout GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference/reference_markers.hmm GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:53:56,554] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:53:56,555] [INFO] Found 6/6 markers.
[2023-06-07 21:53:56,575] [INFO] Query marker FASTA was written to GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/markers.fasta
[2023-06-07 21:53:56,575] [INFO] Task started: Blastn
[2023-06-07 21:53:56,575] [INFO] Running command: blastn -query GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/markers.fasta -db /var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference/reference_markers.fasta -out GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:53:57,196] [INFO] Task succeeded: Blastn
[2023-06-07 21:53:57,199] [INFO] Selected 26 target genomes.
[2023-06-07 21:53:57,199] [INFO] Target genome list was writen to GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/target_genomes.txt
[2023-06-07 21:53:57,203] [INFO] Task started: fastANI
[2023-06-07 21:53:57,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg10d0047f-889c-4b4a-8544-dd04c6b2d01a/GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna.gz --refList GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/target_genomes.txt --output GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:54:12,625] [INFO] Task succeeded: fastANI
[2023-06-07 21:54:12,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:54:12,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:54:12,627] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:54:12,628] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 21:54:12,628] [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
--------------------------------------------------------------------------------
[2023-06-07 21:54:12,630] [INFO] DFAST Taxonomy check result was written to GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/tc_result.tsv
[2023-06-07 21:54:12,630] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:54:12,631] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:54:12,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference/checkm_data
[2023-06-07 21:54:12,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:54:12,654] [INFO] Task started: CheckM
[2023-06-07 21:54:12,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/checkm_input GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/checkm_result
[2023-06-07 21:54:30,700] [INFO] Task succeeded: CheckM
[2023-06-07 21:54:30,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:54:30,719] [INFO] ===== Completeness check finished =====
[2023-06-07 21:54:30,720] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:54:30,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/markers.fasta)
[2023-06-07 21:54:30,720] [INFO] Task started: Blastn
[2023-06-07 21:54:30,720] [INFO] Running command: blastn -query GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/markers.fasta -db /var/lib/cwl/stg5725a447-b006-48f4-9170-e360a64fe867/dqc_reference/reference_markers_gtdb.fasta -out GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:54:31,793] [INFO] Task succeeded: Blastn
[2023-06-07 21:54:31,797] [INFO] Selected 26 target genomes.
[2023-06-07 21:54:31,797] [INFO] Target genome list was writen to GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:54:31,808] [INFO] Task started: fastANI
[2023-06-07 21:54:31,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg10d0047f-889c-4b4a-8544-dd04c6b2d01a/GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna.gz --refList GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/target_genomes_gtdb.txt --output GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:54:41,823] [INFO] Task succeeded: fastANI
[2023-06-07 21:54:41,832] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:54:41,832] [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_900317555.1	s__CAG-791 sp900317555	99.1171	434	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.87	98.02	0.91	0.83	60	conclusive
GCA_900317475.1	s__CAG-791 sp900317475	77.7329	58	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.34	98.93	0.86	0.78	29	-
GCA_900107575.1	s__CAG-791 sp900107575	77.6405	107	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315055.1	s__CAG-791 sp900315055	77.4103	76	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.03	98.45	0.88	0.84	8	-
GCA_000431495.1	s__CAG-791 sp000431495	77.2601	103	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.54	97.54	0.90	0.90	2	-
GCA_002353635.1	s__CAG-791 sp002353635	77.1851	92	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316855.1	s__CAG-791 sp900316855	77.0128	101	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017449745.1	s__CAG-791 sp017449745	76.6876	63	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432565.1	s__CAG-791 sp017432565	76.4349	65	471	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:54:41,834] [INFO] GTDB search result was written to GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/result_gtdb.tsv
[2023-06-07 21:54:41,835] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:54:41,837] [INFO] DFAST_QC result json was written to GCA_902775845.1_Rumen_uncultured_genome_RUG12114_genomic.fna/dqc_result.json
[2023-06-07 21:54:41,837] [INFO] DFAST_QC completed!
[2023-06-07 21:54:41,838] [INFO] Total running time: 0h0m50s