[2023-06-08 09:32:01,820] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:32:01,823] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:32:01,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference
[2023-06-08 09:32:03,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:32:03,478] [INFO] Task started: Prodigal
[2023-06-08 09:32:03,478] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb2144ec-1522-4727-9e08-baffdc729947/GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna.gz | prodigal -d GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/cds.fna -a GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:10,327] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:10,328] [INFO] Task started: HMMsearch
[2023-06-08 09:32:10,328] [INFO] Running command: hmmsearch --tblout GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference/reference_markers.hmm GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:10,651] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:10,652] [INFO] Found 6/6 markers.
[2023-06-08 09:32:10,696] [INFO] Query marker FASTA was written to GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/markers.fasta
[2023-06-08 09:32:10,696] [INFO] Task started: Blastn
[2023-06-08 09:32:10,697] [INFO] Running command: blastn -query GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference/reference_markers.fasta -out GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:13,316] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:13,319] [INFO] Selected 26 target genomes.
[2023-06-08 09:32:13,320] [INFO] Target genome list was writen to GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/target_genomes.txt
[2023-06-08 09:32:13,339] [INFO] Task started: fastANI
[2023-06-08 09:32:13,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb2144ec-1522-4727-9e08-baffdc729947/GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna.gz --refList GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/target_genomes.txt --output GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:32:34,639] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:34,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:32:34,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:32:34,647] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:32:34,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:32:34,648] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	75.7605	64	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:32:34,665] [INFO] DFAST Taxonomy check result was written to GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/tc_result.tsv
[2023-06-08 09:32:34,666] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:32:34,667] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:32:34,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference/checkm_data
[2023-06-08 09:32:34,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:32:34,700] [INFO] Task started: CheckM
[2023-06-08 09:32:34,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/checkm_input GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/checkm_result
[2023-06-08 09:33:00,466] [INFO] Task succeeded: CheckM
[2023-06-08 09:33:00,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:33:00,500] [INFO] ===== Completeness check finished =====
[2023-06-08 09:33:00,501] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:33:00,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/markers.fasta)
[2023-06-08 09:33:00,501] [INFO] Task started: Blastn
[2023-06-08 09:33:00,502] [INFO] Running command: blastn -query GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d63cca2-0601-43b9-b43e-aa37f3eec815/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:33:01,651] [INFO] Task succeeded: Blastn
[2023-06-08 09:33:01,655] [INFO] Selected 23 target genomes.
[2023-06-08 09:33:01,655] [INFO] Target genome list was writen to GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:33:01,664] [INFO] Task started: fastANI
[2023-06-08 09:33:01,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb2144ec-1522-4727-9e08-baffdc729947/GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna.gz --refList GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/target_genomes_gtdb.txt --output GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:33:15,358] [INFO] Task succeeded: fastANI
[2023-06-08 09:33:15,372] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:33:15,373] [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_900316855.1	s__CAG-791 sp900316855	99.9937	813	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_900107575.1	s__CAG-791 sp900107575	77.7407	165	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315055.1	s__CAG-791 sp900315055	77.409	155	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.03	98.45	0.88	0.84	8	-
GCA_900318875.1	s__CAG-791 sp900318875	77.2661	154	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.20	98.52	0.87	0.80	24	-
GCA_000431495.1	s__CAG-791 sp000431495	77.2202	121	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.54	97.54	0.90	0.90	2	-
GCA_900317555.1	s__CAG-791 sp900317555	76.9154	128	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.87	98.02	0.91	0.83	60	-
GCA_017432565.1	s__CAG-791 sp017432565	76.594	90	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449745.1	s__CAG-791 sp017449745	76.4939	85	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781215.1	s__CAG-791 sp902781215	76.4058	82	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.36	96.36	0.81	0.81	2	-
GCF_900101015.1	s__CAG-791 sp900101015	76.128	52	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.38	97.83	0.92	0.75	35	-
GCA_902796425.1	s__CAG-791 sp902796425	75.8161	79	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:33:15,375] [INFO] GTDB search result was written to GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/result_gtdb.tsv
[2023-06-08 09:33:15,375] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:33:15,378] [INFO] DFAST_QC result json was written to GCA_902795145.1_Rumen_uncultured_genome_RUG14031_genomic.fna/dqc_result.json
[2023-06-08 09:33:15,379] [INFO] DFAST_QC completed!
[2023-06-08 09:33:15,379] [INFO] Total running time: 0h1m14s