[2023-06-19 08:51:16,203] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:51:16,209] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:51:16,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference
[2023-06-19 08:51:17,509] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:51:17,510] [INFO] Task started: Prodigal
[2023-06-19 08:51:17,510] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf02bb39-c724-4a4d-9be7-cbdb14d9971c/GCA_014868245.1_ASM1486824v1_genomic.fna.gz | prodigal -d GCA_014868245.1_ASM1486824v1_genomic.fna/cds.fna -a GCA_014868245.1_ASM1486824v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:51:23,517] [INFO] Task succeeded: Prodigal
[2023-06-19 08:51:23,518] [INFO] Task started: HMMsearch
[2023-06-19 08:51:23,518] [INFO] Running command: hmmsearch --tblout GCA_014868245.1_ASM1486824v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference/reference_markers.hmm GCA_014868245.1_ASM1486824v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:51:23,768] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:51:23,770] [INFO] Found 6/6 markers.
[2023-06-19 08:51:23,799] [INFO] Query marker FASTA was written to GCA_014868245.1_ASM1486824v1_genomic.fna/markers.fasta
[2023-06-19 08:51:23,799] [INFO] Task started: Blastn
[2023-06-19 08:51:23,800] [INFO] Running command: blastn -query GCA_014868245.1_ASM1486824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference/reference_markers.fasta -out GCA_014868245.1_ASM1486824v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:24,438] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:24,444] [INFO] Selected 13 target genomes.
[2023-06-19 08:51:24,444] [INFO] Target genome list was writen to GCA_014868245.1_ASM1486824v1_genomic.fna/target_genomes.txt
[2023-06-19 08:51:24,447] [INFO] Task started: fastANI
[2023-06-19 08:51:24,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf02bb39-c724-4a4d-9be7-cbdb14d9971c/GCA_014868245.1_ASM1486824v1_genomic.fna.gz --refList GCA_014868245.1_ASM1486824v1_genomic.fna/target_genomes.txt --output GCA_014868245.1_ASM1486824v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:51:31,808] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:31,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:51:31,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:51:31,817] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 08:51:31,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:51:31,818] [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 bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	97.6092	759	851	95	conclusive
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.6922	130	851	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.673	128	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:51:31,820] [INFO] DFAST Taxonomy check result was written to GCA_014868245.1_ASM1486824v1_genomic.fna/tc_result.tsv
[2023-06-19 08:51:31,820] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:51:31,821] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:51:31,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference/checkm_data
[2023-06-19 08:51:31,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:51:31,862] [INFO] Task started: CheckM
[2023-06-19 08:51:31,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014868245.1_ASM1486824v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014868245.1_ASM1486824v1_genomic.fna/checkm_input GCA_014868245.1_ASM1486824v1_genomic.fna/checkm_result
[2023-06-19 08:51:56,864] [INFO] Task succeeded: CheckM
[2023-06-19 08:51:56,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:51:56,889] [INFO] ===== Completeness check finished =====
[2023-06-19 08:51:56,890] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:51:56,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014868245.1_ASM1486824v1_genomic.fna/markers.fasta)
[2023-06-19 08:51:56,890] [INFO] Task started: Blastn
[2023-06-19 08:51:56,891] [INFO] Running command: blastn -query GCA_014868245.1_ASM1486824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4d2f08-40e7-4d54-96a7-ec7a009cb92d/dqc_reference/reference_markers_gtdb.fasta -out GCA_014868245.1_ASM1486824v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:57,887] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:57,892] [INFO] Selected 18 target genomes.
[2023-06-19 08:51:57,892] [INFO] Target genome list was writen to GCA_014868245.1_ASM1486824v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:51:57,896] [INFO] Task started: fastANI
[2023-06-19 08:51:57,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf02bb39-c724-4a4d-9be7-cbdb14d9971c/GCA_014868245.1_ASM1486824v1_genomic.fna.gz --refList GCA_014868245.1_ASM1486824v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014868245.1_ASM1486824v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:52:05,781] [INFO] Task succeeded: fastANI
[2023-06-19 08:52:05,794] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:52:05,794] [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_000723465.1	s__Ruminococcus_D bicirculans	97.6092	759	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.50	96.68	0.89	0.80	66	conclusive
GCA_900539095.1	s__Ruminococcus_D sp900539095	89.6062	570	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.71	97.55	0.88	0.82	3	-
GCF_900112155.1	s__Ruminococcus_D albus_D	78.3901	164	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318545.1	s__Ruminococcus_D sp900318545	77.9748	138	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.38	97.31	0.84	0.77	8	-
GCF_000621805.1	s__Ruminococcus_D sp000621805	77.9287	122	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626015.1	s__Ruminococcus_D sp017626015	77.9218	158	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319075.1	s__Ruminococcus_D sp900319075	77.9169	115	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.31	96.98	0.90	0.83	16	-
GCA_017484095.1	s__Ruminococcus_D sp017484095	77.8229	153	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391065.1	s__Ruminococcus_D sp002391065	77.7078	140	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179635.2	s__Ruminococcus_D albus	77.6922	130	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.29	97.69	0.91	0.87	8	-
GCF_000526775.1	s__Ruminococcus_D albus_A	77.5403	133	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.64	97.22	0.89	0.80	5	-
GCF_900109655.1	s__Ruminococcus_D albus_B	77.4402	130	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	96.54	96.54	0.90	0.90	2	-
GCA_902767035.1	s__Ruminococcus_D sp902767035	77.2908	119	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067005.1	s__Ruminococcus flavefaciens_AA	77.1518	52	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.27	97.11	0.86	0.81	3	-
GCA_017442845.1	s__Ruminococcus_D sp017442845	76.3381	71	851	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:52:05,797] [INFO] GTDB search result was written to GCA_014868245.1_ASM1486824v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:52:05,797] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:52:05,804] [INFO] DFAST_QC result json was written to GCA_014868245.1_ASM1486824v1_genomic.fna/dqc_result.json
[2023-06-19 08:52:05,804] [INFO] DFAST_QC completed!
[2023-06-19 08:52:05,804] [INFO] Total running time: 0h0m50s