[2023-06-04 23:57:36,091] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:57:36,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:57:36,093] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference
[2023-06-04 23:57:38,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:57:38,137] [INFO] Task started: Prodigal
[2023-06-04 23:57:38,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg34ecfd65-d7dd-4269-b5a9-711bef681a39/GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna.gz | prodigal -d GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/cds.fna -a GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:57:43,163] [INFO] Task succeeded: Prodigal
[2023-06-04 23:57:43,163] [INFO] Task started: HMMsearch
[2023-06-04 23:57:43,163] [INFO] Running command: hmmsearch --tblout GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference/reference_markers.hmm GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:57:43,403] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:57:43,404] [INFO] Found 6/6 markers.
[2023-06-04 23:57:43,428] [INFO] Query marker FASTA was written to GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/markers.fasta
[2023-06-04 23:57:43,429] [INFO] Task started: Blastn
[2023-06-04 23:57:43,429] [INFO] Running command: blastn -query GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference/reference_markers.fasta -out GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:57:44,096] [INFO] Task succeeded: Blastn
[2023-06-04 23:57:44,101] [INFO] Selected 23 target genomes.
[2023-06-04 23:57:44,102] [INFO] Target genome list was writen to GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/target_genomes.txt
[2023-06-04 23:57:44,104] [INFO] Task started: fastANI
[2023-06-04 23:57:44,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg34ecfd65-d7dd-4269-b5a9-711bef681a39/GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna.gz --refList GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/target_genomes.txt --output GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:57:53,870] [INFO] Task succeeded: fastANI
[2023-06-04 23:57:53,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:57:53,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:57:53,883] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:57:53,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 23:57:53,883] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.61	61	525	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.5667	62	525	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.5189	62	525	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3893	58	525	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.2053	64	525	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.1839	52	525	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.7502	50	525	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.7491	50	525	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 23:57:53,886] [INFO] DFAST Taxonomy check result was written to GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/tc_result.tsv
[2023-06-04 23:57:53,886] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:57:53,886] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:57:53,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference/checkm_data
[2023-06-04 23:57:53,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:57:53,910] [INFO] Task started: CheckM
[2023-06-04 23:57:53,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/checkm_input GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/checkm_result
[2023-06-04 23:58:14,834] [INFO] Task succeeded: CheckM
[2023-06-04 23:58:14,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:58:14,856] [INFO] ===== Completeness check finished =====
[2023-06-04 23:58:14,857] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:58:14,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/markers.fasta)
[2023-06-04 23:58:14,857] [INFO] Task started: Blastn
[2023-06-04 23:58:14,858] [INFO] Running command: blastn -query GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d148895-f1b6-45b3-b45e-18390942ebb1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:58:16,052] [INFO] Task succeeded: Blastn
[2023-06-04 23:58:16,057] [INFO] Selected 14 target genomes.
[2023-06-04 23:58:16,057] [INFO] Target genome list was writen to GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:58:16,068] [INFO] Task started: fastANI
[2023-06-04 23:58:16,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg34ecfd65-d7dd-4269-b5a9-711bef681a39/GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna.gz --refList GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/target_genomes_gtdb.txt --output GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:58:21,610] [INFO] Task succeeded: fastANI
[2023-06-04 23:58:21,625] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:58:21,625] [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_900316335.1	s__Faecousia sp900316335	98.3446	457	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.38	98.08	0.86	0.79	12	conclusive
GCA_902795195.1	s__Faecousia sp902795195	80.2431	205	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372735.1	s__Faecousia sp002372735	79.9598	158	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519005.1	s__Faecousia sp017519005	79.7125	196	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.84	97.84	0.75	0.75	2	-
GCA_902767915.1	s__Faecousia sp902767915	79.6844	200	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.86	97.78	0.84	0.82	3	-
GCA_017540945.1	s__Faecousia sp017540945	79.6123	187	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.32	98.32	0.76	0.76	2	-
GCA_017541995.1	s__Faecousia sp017541995	79.5502	214	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292255.1	s__Faecousia sp016292255	79.0945	209	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938625.1	s__Avoscillospira sp017938625	77.5315	50	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002436765.1	s__Faecousia sp002436765	77.5252	74	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_904395865.1	s__Avoscillospira_A sp904395865	77.3148	88	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395905.1	s__Avoscillospira_A sp904395905	76.6004	75	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:58:21,627] [INFO] GTDB search result was written to GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/result_gtdb.tsv
[2023-06-04 23:58:21,628] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:58:21,631] [INFO] DFAST_QC result json was written to GCA_902777035.1_Rumen_uncultured_genome_RUG12230_genomic.fna/dqc_result.json
[2023-06-04 23:58:21,631] [INFO] DFAST_QC completed!
[2023-06-04 23:58:21,631] [INFO] Total running time: 0h0m46s