[2023-06-06 00:03:06,175] [INFO] DFAST_QC pipeline started.
[2023-06-06 00:03:06,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-06 00:03:06,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference
[2023-06-06 00:03:07,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-06 00:03:07,334] [INFO] Task started: Prodigal
[2023-06-06 00:03:07,334] [INFO] Running command: gunzip -c /var/lib/cwl/stge353da27-4624-42af-a157-abeff3843cb1/GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna.gz | prodigal -d GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/cds.fna -a GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-06 00:03:12,143] [INFO] Task succeeded: Prodigal
[2023-06-06 00:03:12,143] [INFO] Task started: HMMsearch
[2023-06-06 00:03:12,143] [INFO] Running command: hmmsearch --tblout GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference/reference_markers.hmm GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/protein.faa > /dev/null
[2023-06-06 00:03:12,320] [INFO] Task succeeded: HMMsearch
[2023-06-06 00:03:12,321] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge353da27-4624-42af-a157-abeff3843cb1/GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna.gz]
[2023-06-06 00:03:12,342] [INFO] Query marker FASTA was written to GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/markers.fasta
[2023-06-06 00:03:12,342] [INFO] Task started: Blastn
[2023-06-06 00:03:12,342] [INFO] Running command: blastn -query GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/markers.fasta -db /var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference/reference_markers.fasta -out GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:03:12,916] [INFO] Task succeeded: Blastn
[2023-06-06 00:03:12,919] [INFO] Selected 19 target genomes.
[2023-06-06 00:03:12,920] [INFO] Target genome list was writen to GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/target_genomes.txt
[2023-06-06 00:03:12,924] [INFO] Task started: fastANI
[2023-06-06 00:03:12,924] [INFO] Running command: fastANI --query /var/lib/cwl/stge353da27-4624-42af-a157-abeff3843cb1/GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna.gz --refList GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/target_genomes.txt --output GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/fastani_result.tsv --threads 1
[2023-06-06 00:03:21,627] [INFO] Task succeeded: fastANI
[2023-06-06 00:03:21,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-06 00:03:21,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-06 00:03:21,635] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-06 00:03:21,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-06 00:03:21,635] [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
Absicoccus porci	strain=YH-panp20	GCA_003725415.1	2486576	2486576	type	True	98.3509	560	617	95	conclusive
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	77.5334	94	617	95	below_threshold
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	77.3509	93	617	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	76.9521	58	617	95	below_threshold
Faecalicoccus acidiformans	strain=DSM 26963	GCA_014202635.1	915173	915173	type	True	76.8687	53	617	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-06 00:03:21,638] [INFO] DFAST Taxonomy check result was written to GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/tc_result.tsv
[2023-06-06 00:03:21,638] [INFO] ===== Taxonomy check completed =====
[2023-06-06 00:03:21,638] [INFO] ===== Start completeness check using CheckM =====
[2023-06-06 00:03:21,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference/checkm_data
[2023-06-06 00:03:21,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-06 00:03:21,777] [INFO] Task started: CheckM
[2023-06-06 00:03:21,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/checkm_input GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/checkm_result
[2023-06-06 00:03:43,485] [INFO] Task succeeded: CheckM
[2023-06-06 00:03:43,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-06 00:03:43,503] [INFO] ===== Completeness check finished =====
[2023-06-06 00:03:43,504] [INFO] ===== Start GTDB Search =====
[2023-06-06 00:03:43,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/markers.fasta)
[2023-06-06 00:03:43,504] [INFO] Task started: Blastn
[2023-06-06 00:03:43,504] [INFO] Running command: blastn -query GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/markers.fasta -db /var/lib/cwl/stgaffd24f7-92bf-4a32-8860-73cbaeee8c09/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:03:44,350] [INFO] Task succeeded: Blastn
[2023-06-06 00:03:44,353] [INFO] Selected 17 target genomes.
[2023-06-06 00:03:44,354] [INFO] Target genome list was writen to GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/target_genomes_gtdb.txt
[2023-06-06 00:03:44,403] [INFO] Task started: fastANI
[2023-06-06 00:03:44,403] [INFO] Running command: fastANI --query /var/lib/cwl/stge353da27-4624-42af-a157-abeff3843cb1/GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna.gz --refList GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/target_genomes_gtdb.txt --output GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-06 00:03:49,602] [INFO] Task succeeded: fastANI
[2023-06-06 00:03:49,613] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-06 00:03:49,613] [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_003725415.1	s__Absicoccus porci	98.3509	560	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	98.56	98.14	0.93	0.90	14	conclusive
GCA_003480165.1	s__Absicoccus sp000434355	78.4476	173	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	99.44	99.16	0.95	0.93	5	-
GCF_000156655.1	s__Holdemanella biformis	77.5334	94	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
GCA_900547815.1	s__Holdemanella sp900547815	77.4375	77	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
GCF_009696075.1	s__Holdemanella porci	77.3509	93	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	-
GCF_000420345.1	s__Faecalicoccus pleomorphus	77.2097	69	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	97.06	96.03	0.88	0.84	9	-
GCA_900754615.1	s__Holdemanella sp900754615	77.0512	88	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902399855.1	s__Faecalicoccus sp900546545	77.0148	73	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	99.03	98.24	0.89	0.80	8	-
GCF_009696175.1	s__Floccifex porci	76.9521	58	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex	95.0	99.09	99.09	0.94	0.94	2	-
GCF_014202635.1	s__Faecalicoccus acidiformans	76.8687	53	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0	98.13	97.66	0.90	0.87	3	-
GCA_900556915.1	s__Holdemanella sp900556915	76.6209	55	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	-
GCF_000469305.1	s__Faecalitalea cylindroides	76.5313	59	617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalitalea	95.0	98.51	97.31	0.84	0.75	12	-
--------------------------------------------------------------------------------
[2023-06-06 00:03:49,615] [INFO] GTDB search result was written to GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/result_gtdb.tsv
[2023-06-06 00:03:49,616] [INFO] ===== GTDB Search completed =====
[2023-06-06 00:03:49,620] [INFO] DFAST_QC result json was written to GCA_902781835.1_Rumen_uncultured_genome_RUG12706_genomic.fna/dqc_result.json
[2023-06-06 00:03:49,620] [INFO] DFAST_QC completed!
[2023-06-06 00:03:49,620] [INFO] Total running time: 0h0m43s