[2023-06-05 19:01:14,018] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:14,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:14,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference
[2023-06-05 19:01:15,233] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:15,234] [INFO] Task started: Prodigal
[2023-06-05 19:01:15,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg2173f500-17fd-419c-ad57-673f188c31d9/GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna.gz | prodigal -d GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/cds.fna -a GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:01:17,834] [INFO] Task succeeded: Prodigal
[2023-06-05 19:01:17,834] [INFO] Task started: HMMsearch
[2023-06-05 19:01:17,835] [INFO] Running command: hmmsearch --tblout GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference/reference_markers.hmm GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:01:18,040] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:01:18,041] [INFO] Found 6/6 markers.
[2023-06-05 19:01:18,060] [INFO] Query marker FASTA was written to GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/markers.fasta
[2023-06-05 19:01:18,060] [INFO] Task started: Blastn
[2023-06-05 19:01:18,060] [INFO] Running command: blastn -query GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/markers.fasta -db /var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference/reference_markers.fasta -out GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:18,647] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:18,651] [INFO] Selected 20 target genomes.
[2023-06-05 19:01:18,652] [INFO] Target genome list was writen to GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/target_genomes.txt
[2023-06-05 19:01:18,663] [INFO] Task started: fastANI
[2023-06-05 19:01:18,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg2173f500-17fd-419c-ad57-673f188c31d9/GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna.gz --refList GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/target_genomes.txt --output GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:01:31,075] [INFO] Task succeeded: fastANI
[2023-06-05 19:01:31,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:01:31,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:01:31,079] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:01:31,079] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 19:01:31,079] [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 19:01:31,082] [INFO] DFAST Taxonomy check result was written to GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/tc_result.tsv
[2023-06-05 19:01:31,083] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:01:31,083] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:01:31,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference/checkm_data
[2023-06-05 19:01:31,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:01:31,105] [INFO] Task started: CheckM
[2023-06-05 19:01:31,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/checkm_input GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/checkm_result
[2023-06-05 19:01:46,652] [INFO] Task succeeded: CheckM
[2023-06-05 19:01:46,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 19:01:46,675] [INFO] ===== Completeness check finished =====
[2023-06-05 19:01:46,675] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:01:46,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/markers.fasta)
[2023-06-05 19:01:46,676] [INFO] Task started: Blastn
[2023-06-05 19:01:46,676] [INFO] Running command: blastn -query GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/markers.fasta -db /var/lib/cwl/stg4180b15a-e3ac-498e-8221-c6f205630b6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:47,489] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:47,494] [INFO] Selected 10 target genomes.
[2023-06-05 19:01:47,495] [INFO] Target genome list was writen to GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:01:47,508] [INFO] Task started: fastANI
[2023-06-05 19:01:47,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg2173f500-17fd-419c-ad57-673f188c31d9/GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna.gz --refList GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/target_genomes_gtdb.txt --output GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:01:50,019] [INFO] Task succeeded: fastANI
[2023-06-05 19:01:50,033] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:01:50,033] [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_902767385.1	s__UBA1436 sp902767385	100.0	306	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017961295.1	s__UBA1436 sp017961295	89.701	183	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761975.1	s__UBA1436 sp902761975	80.641	210	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961585.1	s__UBA1436 sp017961585	79.2089	174	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	98.69	98.69	0.94	0.94	2	-
GCA_900319885.1	s__UBA1436 sp900319885	78.8395	136	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	97.95	97.18	0.91	0.77	6	-
GCA_900319325.1	s__UBA1436 sp900319325	78.5456	122	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902798835.1	s__UBA1436 sp902798835	78.514	151	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	95.64	95.64	0.89	0.89	2	-
GCA_017475405.1	s__UBA1436 sp017475405	78.2312	144	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315845.1	s__UBA1436 sp900315845	77.5944	86	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015062115.1	s__UBA1436 sp015062115	77.2494	88	314	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	98.51	98.51	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-05 19:01:50,035] [INFO] GTDB search result was written to GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/result_gtdb.tsv
[2023-06-05 19:01:50,036] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:01:50,039] [INFO] DFAST_QC result json was written to GCA_902767385.1_Rumen_uncultured_genome_RUG11256_genomic.fna/dqc_result.json
[2023-06-05 19:01:50,039] [INFO] DFAST_QC completed!
[2023-06-05 19:01:50,039] [INFO] Total running time: 0h0m36s