[2023-06-05 00:01:52,144] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:01:52,160] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:01:52,160] [INFO] DQC Reference Directory: /var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference
[2023-06-05 00:01:53,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:01:53,498] [INFO] Task started: Prodigal
[2023-06-05 00:01:53,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg827fc7ea-ad0b-4635-9662-8e88ede957e3/GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna.gz | prodigal -d GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/cds.fna -a GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:01:58,015] [INFO] Task succeeded: Prodigal
[2023-06-05 00:01:58,015] [INFO] Task started: HMMsearch
[2023-06-05 00:01:58,015] [INFO] Running command: hmmsearch --tblout GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference/reference_markers.hmm GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:01:58,302] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:01:58,304] [INFO] Found 6/6 markers.
[2023-06-05 00:01:58,329] [INFO] Query marker FASTA was written to GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/markers.fasta
[2023-06-05 00:01:58,329] [INFO] Task started: Blastn
[2023-06-05 00:01:58,329] [INFO] Running command: blastn -query GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference/reference_markers.fasta -out GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:01:58,987] [INFO] Task succeeded: Blastn
[2023-06-05 00:01:58,991] [INFO] Selected 19 target genomes.
[2023-06-05 00:01:58,991] [INFO] Target genome list was writen to GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/target_genomes.txt
[2023-06-05 00:01:58,998] [INFO] Task started: fastANI
[2023-06-05 00:01:58,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg827fc7ea-ad0b-4635-9662-8e88ede957e3/GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna.gz --refList GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/target_genomes.txt --output GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:02:11,444] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:11,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:02:11,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:02:11,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:02:11,447] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:02:11,447] [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
--------------------------------------------------------------------------------
[2023-06-05 00:02:11,450] [INFO] DFAST Taxonomy check result was written to GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/tc_result.tsv
[2023-06-05 00:02:11,450] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:02:11,451] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:02:11,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference/checkm_data
[2023-06-05 00:02:11,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:02:11,485] [INFO] Task started: CheckM
[2023-06-05 00:02:11,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/checkm_input GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/checkm_result
[2023-06-05 00:02:32,617] [INFO] Task succeeded: CheckM
[2023-06-05 00:02:32,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:02:32,639] [INFO] ===== Completeness check finished =====
[2023-06-05 00:02:32,640] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:02:32,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/markers.fasta)
[2023-06-05 00:02:32,641] [INFO] Task started: Blastn
[2023-06-05 00:02:32,641] [INFO] Running command: blastn -query GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b7aff7-cca4-4b72-906f-50c050f1b523/dqc_reference/reference_markers_gtdb.fasta -out GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:33,710] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:33,715] [INFO] Selected 15 target genomes.
[2023-06-05 00:02:33,716] [INFO] Target genome list was writen to GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:02:33,730] [INFO] Task started: fastANI
[2023-06-05 00:02:33,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg827fc7ea-ad0b-4635-9662-8e88ede957e3/GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna.gz --refList GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/target_genomes_gtdb.txt --output GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:02:40,600] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:40,618] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:02:40,618] [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_900317815.1	s__RUG592 sp900317815	100.0	633	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	99.43	98.86	0.91	0.82	3	conclusive
GCA_900317025.1	s__RUG592 sp900317025	80.0479	271	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	99.45	99.45	0.94	0.94	2	-
GCA_902792115.1	s__RUG592 sp902792115	79.5501	235	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785425.1	s__RUG592 sp902785425	79.3584	277	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313125.1	s__RUG592 sp900313125	79.1986	201	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	100.00	100.00	0.98	0.98	2	-
GCA_902779615.1	s__RUG592 sp902779615	78.1667	157	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773165.1	s__RUG592 sp902773165	77.9486	150	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802975.1	s__RUG592 sp902802975	77.4998	95	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	99.00	99.00	0.72	0.72	2	-
GCA_902773045.1	s__RUG592 sp902773045	76.5256	94	639	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:02:40,621] [INFO] GTDB search result was written to GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/result_gtdb.tsv
[2023-06-05 00:02:40,621] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:02:40,625] [INFO] DFAST_QC result json was written to GCA_902759635.1_Rumen_uncultured_genome_RUG10481_genomic.fna/dqc_result.json
[2023-06-05 00:02:40,626] [INFO] DFAST_QC completed!
[2023-06-05 00:02:40,626] [INFO] Total running time: 0h0m48s