[2023-06-05 02:43:40,837] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:43:40,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:43:40,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference
[2023-06-05 02:43:42,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:43:42,104] [INFO] Task started: Prodigal
[2023-06-05 02:43:42,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg231bedd9-de01-4870-8b66-de827d506980/GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna.gz | prodigal -d GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/cds.fna -a GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:43:50,098] [INFO] Task succeeded: Prodigal
[2023-06-05 02:43:50,099] [INFO] Task started: HMMsearch
[2023-06-05 02:43:50,099] [INFO] Running command: hmmsearch --tblout GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference/reference_markers.hmm GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:43:50,367] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:43:50,368] [INFO] Found 6/6 markers.
[2023-06-05 02:43:50,402] [INFO] Query marker FASTA was written to GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/markers.fasta
[2023-06-05 02:43:50,402] [INFO] Task started: Blastn
[2023-06-05 02:43:50,403] [INFO] Running command: blastn -query GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference/reference_markers.fasta -out GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:43:51,036] [INFO] Task succeeded: Blastn
[2023-06-05 02:43:51,040] [INFO] Selected 28 target genomes.
[2023-06-05 02:43:51,041] [INFO] Target genome list was writen to GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/target_genomes.txt
[2023-06-05 02:43:51,047] [INFO] Task started: fastANI
[2023-06-05 02:43:51,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg231bedd9-de01-4870-8b66-de827d506980/GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna.gz --refList GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/target_genomes.txt --output GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:44:06,585] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:06,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:44:06,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:44:06,588] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:44:06,588] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:44:06,588] [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 02:44:06,591] [INFO] DFAST Taxonomy check result was written to GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/tc_result.tsv
[2023-06-05 02:44:06,592] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:44:06,592] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:44:06,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference/checkm_data
[2023-06-05 02:44:06,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:44:06,627] [INFO] Task started: CheckM
[2023-06-05 02:44:06,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/checkm_input GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/checkm_result
[2023-06-05 02:44:35,387] [INFO] Task succeeded: CheckM
[2023-06-05 02:44:35,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:44:35,410] [INFO] ===== Completeness check finished =====
[2023-06-05 02:44:35,410] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:44:35,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/markers.fasta)
[2023-06-05 02:44:35,411] [INFO] Task started: Blastn
[2023-06-05 02:44:35,411] [INFO] Running command: blastn -query GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb78b46-3041-4183-9b95-c0e8565ea726/dqc_reference/reference_markers_gtdb.fasta -out GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:44:36,332] [INFO] Task succeeded: Blastn
[2023-06-05 02:44:36,336] [INFO] Selected 11 target genomes.
[2023-06-05 02:44:36,337] [INFO] Target genome list was writen to GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:44:36,345] [INFO] Task started: fastANI
[2023-06-05 02:44:36,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg231bedd9-de01-4870-8b66-de827d506980/GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna.gz --refList GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/target_genomes_gtdb.txt --output GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:44:43,435] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:43,450] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:44:43,451] [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_902793605.1	s__GCA-900199385 sp900320755	98.4431	849	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.77	98.33	0.88	0.86	8	conclusive
GCA_900315315.1	s__GCA-900199385 sp900315315	83.0218	560	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017512985.1	s__GCA-900199385 sp017512985	80.8308	381	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017569305.1	s__GCA-900199385 sp900322155	80.3994	363	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.53	98.29	0.93	0.91	5	-
GCA_018118585.1	s__GCA-900199385 sp900176495	80.2483	382	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017427165.1	s__GCA-900199385 sp017427165	80.1762	245	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315675.1	s__GCA-900199385 sp900315675	80.1092	378	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.62	97.73	0.95	0.88	5	-
GCA_902764875.1	s__GCA-900199385 sp902764875	79.8394	321	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	96.75	96.19	0.79	0.75	4	-
GCA_017569285.1	s__GCA-900199385 sp017569285	79.8205	303	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615475.1	s__GCA-900199385 sp017615475	79.6773	230	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447185.1	s__GCA-900199385 sp017447185	79.5163	303	985	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:44:43,453] [INFO] GTDB search result was written to GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/result_gtdb.tsv
[2023-06-05 02:44:43,454] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:44:43,457] [INFO] DFAST_QC result json was written to GCA_902780755.1_Rumen_uncultured_genome_RUG12606_genomic.fna/dqc_result.json
[2023-06-05 02:44:43,457] [INFO] DFAST_QC completed!
[2023-06-05 02:44:43,457] [INFO] Total running time: 0h1m3s