[2023-06-08 04:16:21,646] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:16:21,648] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:16:21,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference
[2023-06-08 04:16:22,922] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:16:22,923] [INFO] Task started: Prodigal
[2023-06-08 04:16:22,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3d21e7b-e456-4bc5-84a7-ae8ed61b8846/GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna.gz | prodigal -d GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/cds.fna -a GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:16:41,905] [INFO] Task succeeded: Prodigal
[2023-06-08 04:16:41,905] [INFO] Task started: HMMsearch
[2023-06-08 04:16:41,906] [INFO] Running command: hmmsearch --tblout GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference/reference_markers.hmm GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:16:42,217] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:16:42,219] [INFO] Found 6/6 markers.
[2023-06-08 04:16:42,249] [INFO] Query marker FASTA was written to GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/markers.fasta
[2023-06-08 04:16:42,250] [INFO] Task started: Blastn
[2023-06-08 04:16:42,250] [INFO] Running command: blastn -query GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference/reference_markers.fasta -out GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:16:42,896] [INFO] Task succeeded: Blastn
[2023-06-08 04:16:42,900] [INFO] Selected 26 target genomes.
[2023-06-08 04:16:42,901] [INFO] Target genome list was writen to GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/target_genomes.txt
[2023-06-08 04:16:42,904] [INFO] Task started: fastANI
[2023-06-08 04:16:42,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3d21e7b-e456-4bc5-84a7-ae8ed61b8846/GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna.gz --refList GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/target_genomes.txt --output GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:16:56,440] [INFO] Task succeeded: fastANI
[2023-06-08 04:16:56,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:16:56,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:16:56,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:16:56,444] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 04:16:56,444] [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
--------------------------------------------------------------------------------
[2023-06-08 04:16:56,446] [INFO] DFAST Taxonomy check result was written to GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/tc_result.tsv
[2023-06-08 04:16:56,447] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:16:56,448] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:16:56,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference/checkm_data
[2023-06-08 04:16:56,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:16:56,486] [INFO] Task started: CheckM
[2023-06-08 04:16:56,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/checkm_input GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/checkm_result
[2023-06-08 04:17:49,920] [INFO] Task succeeded: CheckM
[2023-06-08 04:17:49,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:17:49,936] [INFO] ===== Completeness check finished =====
[2023-06-08 04:17:49,937] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:17:49,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/markers.fasta)
[2023-06-08 04:17:49,937] [INFO] Task started: Blastn
[2023-06-08 04:17:49,938] [INFO] Running command: blastn -query GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e4fbaf4-bf7d-4c8c-b620-e90afee7acd9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:17:50,839] [INFO] Task succeeded: Blastn
[2023-06-08 04:17:50,843] [INFO] Selected 9 target genomes.
[2023-06-08 04:17:50,844] [INFO] Target genome list was writen to GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:17:50,844] [INFO] Task started: fastANI
[2023-06-08 04:17:50,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3d21e7b-e456-4bc5-84a7-ae8ed61b8846/GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna.gz --refList GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/target_genomes_gtdb.txt --output GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:17:57,211] [INFO] Task succeeded: fastANI
[2023-06-08 04:17:57,225] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:17:57,225] [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_900317125.1	s__UBA1711 sp900317125	100.0	961	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	96.93	96.01	0.87	0.83	22	conclusive
GCA_017550405.1	s__UBA1711 sp017550405	92.855	792	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002309955.1	s__UBA1711 sp002309955	84.1877	485	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.92	97.92	0.81	0.81	2	-
GCA_017530105.1	s__UBA1711 sp017530105	83.4385	503	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318175.1	s__UBA1711 sp900318175	83.2589	573	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.21	97.84	0.90	0.87	10	-
GCA_902790215.1	s__UBA1711 sp902790215	82.8774	577	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.42	97.21	0.88	0.83	8	-
GCA_900317955.1	s__UBA1711 sp900317955	82.1273	482	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.66	97.32	0.93	0.86	3	-
GCA_017479705.1	s__UBA1711 sp017479705	81.5902	402	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354035.1	s__UBA1711 sp002354035	81.3343	524	963	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.39	99.39	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-08 04:17:57,227] [INFO] GTDB search result was written to GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/result_gtdb.tsv
[2023-06-08 04:17:57,227] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:17:57,240] [INFO] DFAST_QC result json was written to GCA_902755415.1_Rumen_uncultured_genome_RUG10054_genomic.fna/dqc_result.json
[2023-06-08 04:17:57,241] [INFO] DFAST_QC completed!
[2023-06-08 04:17:57,241] [INFO] Total running time: 0h1m36s