[2023-06-05 19:02:14,150] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:02:14,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:02:14,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference
[2023-06-05 19:02:15,328] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:02:15,329] [INFO] Task started: Prodigal
[2023-06-05 19:02:15,329] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc65c5de-db9d-41ab-98b3-68bfde61751e/GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna.gz | prodigal -d GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/cds.fna -a GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:02:24,453] [INFO] Task succeeded: Prodigal
[2023-06-05 19:02:24,454] [INFO] Task started: HMMsearch
[2023-06-05 19:02:24,454] [INFO] Running command: hmmsearch --tblout GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference/reference_markers.hmm GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:02:24,719] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:02:24,721] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfc65c5de-db9d-41ab-98b3-68bfde61751e/GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna.gz]
[2023-06-05 19:02:24,752] [INFO] Query marker FASTA was written to GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/markers.fasta
[2023-06-05 19:02:24,753] [INFO] Task started: Blastn
[2023-06-05 19:02:24,753] [INFO] Running command: blastn -query GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/markers.fasta -db /var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference/reference_markers.fasta -out GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:25,428] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:25,433] [INFO] Selected 21 target genomes.
[2023-06-05 19:02:25,433] [INFO] Target genome list was writen to GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/target_genomes.txt
[2023-06-05 19:02:25,442] [INFO] Task started: fastANI
[2023-06-05 19:02:25,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc65c5de-db9d-41ab-98b3-68bfde61751e/GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna.gz --refList GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/target_genomes.txt --output GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:02:38,437] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:38,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:02:38,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:02:38,447] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:02:38,448] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:02:38,448] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.2133	55	989	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	75.3958	52	989	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.8269	60	989	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	74.7626	57	989	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:02:38,451] [INFO] DFAST Taxonomy check result was written to GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/tc_result.tsv
[2023-06-05 19:02:38,452] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:02:38,452] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:02:38,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference/checkm_data
[2023-06-05 19:02:38,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:02:38,491] [INFO] Task started: CheckM
[2023-06-05 19:02:38,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/checkm_input GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/checkm_result
[2023-06-05 19:03:09,191] [INFO] Task succeeded: CheckM
[2023-06-05 19:03:09,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:03:09,213] [INFO] ===== Completeness check finished =====
[2023-06-05 19:03:09,214] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:03:09,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/markers.fasta)
[2023-06-05 19:03:09,214] [INFO] Task started: Blastn
[2023-06-05 19:03:09,214] [INFO] Running command: blastn -query GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/markers.fasta -db /var/lib/cwl/stg30033eec-165a-4e98-b9b0-c7e0d8f45791/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:03:10,362] [INFO] Task succeeded: Blastn
[2023-06-05 19:03:10,367] [INFO] Selected 9 target genomes.
[2023-06-05 19:03:10,367] [INFO] Target genome list was writen to GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:03:10,376] [INFO] Task started: fastANI
[2023-06-05 19:03:10,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc65c5de-db9d-41ab-98b3-68bfde61751e/GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna.gz --refList GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/target_genomes_gtdb.txt --output GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:03:21,071] [INFO] Task succeeded: fastANI
[2023-06-05 19:03:21,089] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:03:21,089] [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_900318045.1	s__UBA2862 sp900318045	97.7416	690	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.18	97.25	0.80	0.71	7	conclusive
GCA_902798105.1	s__UBA2862 sp902798105	89.9253	709	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.82	0.82	2	-
GCA_017512905.1	s__UBA2862 sp017512905	86.5634	611	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.84	0.84	2	-
GCA_017432405.1	s__UBA2862 sp017432405	86.4158	632	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765305.1	s__UBA2862 sp902765305	86.3191	660	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.39	97.59	0.81	0.77	4	-
GCA_902801165.1	s__UBA2862 sp902801165	82.8126	514	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799045.1	s__UBA2862 sp902799045	82.3084	455	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540445.1	s__UBA2862 sp017540445	82.3028	427	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778045.1	s__UBA2862 sp902778045	82.0688	437	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 19:03:21,092] [INFO] GTDB search result was written to GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/result_gtdb.tsv
[2023-06-05 19:03:21,092] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:03:21,097] [INFO] DFAST_QC result json was written to GCA_902784635.1_Rumen_uncultured_genome_RUG12987_genomic.fna/dqc_result.json
[2023-06-05 19:03:21,097] [INFO] DFAST_QC completed!
[2023-06-05 19:03:21,097] [INFO] Total running time: 0h1m7s