[2023-06-05 06:34:51,199] [INFO] DFAST_QC pipeline started.
[2023-06-05 06:34:51,201] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 06:34:51,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference
[2023-06-05 06:34:53,541] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 06:34:53,542] [INFO] Task started: Prodigal
[2023-06-05 06:34:53,542] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8e8e96e-9da2-4e76-bb6b-8a80ac3f52da/GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna.gz | prodigal -d GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/cds.fna -a GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 06:34:56,983] [INFO] Task succeeded: Prodigal
[2023-06-05 06:34:56,983] [INFO] Task started: HMMsearch
[2023-06-05 06:34:56,984] [INFO] Running command: hmmsearch --tblout GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference/reference_markers.hmm GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/protein.faa > /dev/null
[2023-06-05 06:34:57,235] [INFO] Task succeeded: HMMsearch
[2023-06-05 06:34:57,236] [INFO] Found 6/6 markers.
[2023-06-05 06:34:57,262] [INFO] Query marker FASTA was written to GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/markers.fasta
[2023-06-05 06:34:57,262] [INFO] Task started: Blastn
[2023-06-05 06:34:57,262] [INFO] Running command: blastn -query GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/markers.fasta -db /var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference/reference_markers.fasta -out GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:34:57,861] [INFO] Task succeeded: Blastn
[2023-06-05 06:34:57,865] [INFO] Selected 20 target genomes.
[2023-06-05 06:34:57,866] [INFO] Target genome list was writen to GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/target_genomes.txt
[2023-06-05 06:34:57,870] [INFO] Task started: fastANI
[2023-06-05 06:34:57,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e8e96e-9da2-4e76-bb6b-8a80ac3f52da/GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna.gz --refList GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/target_genomes.txt --output GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 06:35:06,491] [INFO] Task succeeded: fastANI
[2023-06-05 06:35:06,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 06:35:06,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 06:35:06,499] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 06:35:06,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 06:35:06,500] [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
Ruminococcus bovis	strain=JE7A12	GCA_005601135.1	2564099	2564099	type	True	98.5442	592	637	95	conclusive
--------------------------------------------------------------------------------
[2023-06-05 06:35:06,502] [INFO] DFAST Taxonomy check result was written to GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/tc_result.tsv
[2023-06-05 06:35:06,503] [INFO] ===== Taxonomy check completed =====
[2023-06-05 06:35:06,503] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 06:35:06,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference/checkm_data
[2023-06-05 06:35:06,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 06:35:06,533] [INFO] Task started: CheckM
[2023-06-05 06:35:06,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/checkm_input GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/checkm_result
[2023-06-05 06:35:24,844] [INFO] Task succeeded: CheckM
[2023-06-05 06:35:24,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 06:35:24,869] [INFO] ===== Completeness check finished =====
[2023-06-05 06:35:24,869] [INFO] ===== Start GTDB Search =====
[2023-06-05 06:35:24,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/markers.fasta)
[2023-06-05 06:35:24,870] [INFO] Task started: Blastn
[2023-06-05 06:35:24,870] [INFO] Running command: blastn -query GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/markers.fasta -db /var/lib/cwl/stg61e45c0e-52f9-4640-949c-76251d4d8fb2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:35:25,836] [INFO] Task succeeded: Blastn
[2023-06-05 06:35:25,841] [INFO] Selected 21 target genomes.
[2023-06-05 06:35:25,841] [INFO] Target genome list was writen to GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 06:35:25,851] [INFO] Task started: fastANI
[2023-06-05 06:35:25,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e8e96e-9da2-4e76-bb6b-8a80ac3f52da/GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna.gz --refList GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/target_genomes_gtdb.txt --output GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 06:35:33,553] [INFO] Task succeeded: fastANI
[2023-06-05 06:35:33,567] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 06:35:33,567] [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
GCF_005601135.1	s__Ruminococcus_E sp900314705	98.5782	591	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	96.56	95.43	0.90	0.83	11	conclusive
GCA_017458105.1	s__Ruminococcus_E sp017458105	77.5594	98	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435335.1	s__CAG-964 sp000435335	77.2098	61	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	99.05	99.03	0.94	0.93	3	-
GCF_003438075.1	s__Ruminococcus_E sp003438075	77.089	87	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.49	97.62	0.94	0.88	5	-
GCA_017473555.1	s__Ruminococcus_E sp017473555	77.0791	52	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014288065.1	s__Ruminococcus_E sp003526955	76.9807	81	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.97	97.37	0.85	0.74	16	-
GCA_017410265.1	s__Ruminococcus_E sp017410265	76.8816	52	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.82	97.82	0.84	0.84	2	-
GCF_002834235.1	s__Ruminococcus_E bromii_B	76.668	75	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.64	96.93	0.86	0.80	74	-
--------------------------------------------------------------------------------
[2023-06-05 06:35:33,569] [INFO] GTDB search result was written to GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/result_gtdb.tsv
[2023-06-05 06:35:33,570] [INFO] ===== GTDB Search completed =====
[2023-06-05 06:35:33,572] [INFO] DFAST_QC result json was written to GCA_902767995.1_Rumen_uncultured_genome_RUG11320_genomic.fna/dqc_result.json
[2023-06-05 06:35:33,572] [INFO] DFAST_QC completed!
[2023-06-05 06:35:33,573] [INFO] Total running time: 0h0m42s