[2023-06-07 23:15:34,016] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:15:34,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:15:34,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference
[2023-06-07 23:15:35,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:15:35,512] [INFO] Task started: Prodigal
[2023-06-07 23:15:35,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg09f04897-2c49-47cf-b028-2a8006d808e4/GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna.gz | prodigal -d GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/cds.fna -a GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:15:40,068] [INFO] Task succeeded: Prodigal
[2023-06-07 23:15:40,069] [INFO] Task started: HMMsearch
[2023-06-07 23:15:40,069] [INFO] Running command: hmmsearch --tblout GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference/reference_markers.hmm GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:15:40,311] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:15:40,313] [INFO] Found 6/6 markers.
[2023-06-07 23:15:40,336] [INFO] Query marker FASTA was written to GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/markers.fasta
[2023-06-07 23:15:40,336] [INFO] Task started: Blastn
[2023-06-07 23:15:40,336] [INFO] Running command: blastn -query GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/markers.fasta -db /var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference/reference_markers.fasta -out GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:15:40,974] [INFO] Task succeeded: Blastn
[2023-06-07 23:15:40,979] [INFO] Selected 22 target genomes.
[2023-06-07 23:15:40,979] [INFO] Target genome list was writen to GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/target_genomes.txt
[2023-06-07 23:15:40,996] [INFO] Task started: fastANI
[2023-06-07 23:15:40,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg09f04897-2c49-47cf-b028-2a8006d808e4/GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna.gz --refList GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/target_genomes.txt --output GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:15:53,099] [INFO] Task succeeded: fastANI
[2023-06-07 23:15:53,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:15:53,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:15:53,103] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:15:53,103] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 23:15:53,103] [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 23:15:53,106] [INFO] DFAST Taxonomy check result was written to GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/tc_result.tsv
[2023-06-07 23:15:53,107] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:15:53,107] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:15:53,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference/checkm_data
[2023-06-07 23:15:53,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:15:53,148] [INFO] Task started: CheckM
[2023-06-07 23:15:53,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/checkm_input GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/checkm_result
[2023-06-07 23:16:13,841] [INFO] Task succeeded: CheckM
[2023-06-07 23:16:13,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:16:13,861] [INFO] ===== Completeness check finished =====
[2023-06-07 23:16:13,861] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:16:13,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/markers.fasta)
[2023-06-07 23:16:13,862] [INFO] Task started: Blastn
[2023-06-07 23:16:13,862] [INFO] Running command: blastn -query GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/markers.fasta -db /var/lib/cwl/stgb72b5c61-8fa2-4d98-9077-982f854cfb77/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:14,934] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:14,944] [INFO] Selected 17 target genomes.
[2023-06-07 23:16:14,944] [INFO] Target genome list was writen to GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:16:14,954] [INFO] Task started: fastANI
[2023-06-07 23:16:14,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg09f04897-2c49-47cf-b028-2a8006d808e4/GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna.gz --refList GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/target_genomes_gtdb.txt --output GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:16:21,456] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:21,472] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:16:21,472] [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_900322145.1	s__UBA1213 sp900322145	98.8172	470	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	98.92	98.22	0.85	0.77	17	conclusive
GCA_902803125.1	s__UBA1213 sp902803125	79.1609	209	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785765.1	s__UBA1213 sp902785765	78.6329	213	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803585.1	s__UBA1213 sp902803585	78.5674	225	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900322105.1	s__UBA1213 sp900322105	77.9698	128	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	98.51	97.51	0.88	0.75	10	-
GCA_902772955.1	s__UBA1213 sp902772955	77.8279	142	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802985.1	s__UBA1213 sp902802985	77.3179	77	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002308635.1	s__UBA1213 sp002308635	77.27	102	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.41	99.41	0.75	0.75	2	-
GCA_900316925.1	s__UBA1213 sp900316925	77.2149	130	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.79	99.79	0.89	0.89	2	-
GCA_002350705.1	s__UBA1213 sp002350705	76.8298	93	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.87	99.87	0.91	0.91	2	-
GCA_002351795.1	s__UBA1213 sp002351795	76.5467	54	584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.44	99.44	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-07 23:16:21,474] [INFO] GTDB search result was written to GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/result_gtdb.tsv
[2023-06-07 23:16:21,474] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:16:21,477] [INFO] DFAST_QC result json was written to GCA_902763795.1_Rumen_uncultured_genome_RUG10888_genomic.fna/dqc_result.json
[2023-06-07 23:16:21,477] [INFO] DFAST_QC completed!
[2023-06-07 23:16:21,477] [INFO] Total running time: 0h0m47s