[2023-06-05 02:43:47,443] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:43:47,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:43:47,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference
[2023-06-05 02:43:49,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:43:49,308] [INFO] Task started: Prodigal
[2023-06-05 02:43:49,309] [INFO] Running command: gunzip -c /var/lib/cwl/stgc22e0104-5dd3-465d-9f73-16013346176a/GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna.gz | prodigal -d GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/cds.fna -a GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:43:54,790] [INFO] Task succeeded: Prodigal
[2023-06-05 02:43:54,791] [INFO] Task started: HMMsearch
[2023-06-05 02:43:54,791] [INFO] Running command: hmmsearch --tblout GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference/reference_markers.hmm GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:43:55,040] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:43:55,042] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc22e0104-5dd3-465d-9f73-16013346176a/GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna.gz]
[2023-06-05 02:43:55,068] [INFO] Query marker FASTA was written to GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/markers.fasta
[2023-06-05 02:43:55,068] [INFO] Task started: Blastn
[2023-06-05 02:43:55,069] [INFO] Running command: blastn -query GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/markers.fasta -db /var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference/reference_markers.fasta -out GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:43:55,692] [INFO] Task succeeded: Blastn
[2023-06-05 02:43:55,697] [INFO] Selected 23 target genomes.
[2023-06-05 02:43:55,697] [INFO] Target genome list was writen to GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/target_genomes.txt
[2023-06-05 02:43:55,702] [INFO] Task started: fastANI
[2023-06-05 02:43:55,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgc22e0104-5dd3-465d-9f73-16013346176a/GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna.gz --refList GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/target_genomes.txt --output GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:44:07,387] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:07,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:44:07,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:44:07,398] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:44:07,399] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:44:07,399] [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
Succiniclasticum ruminis	strain=DSM 9236	GCA_900112895.1	40841	40841	suspected-type	True	86.3967	456	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:44:07,402] [INFO] DFAST Taxonomy check result was written to GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/tc_result.tsv
[2023-06-05 02:44:07,402] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:44:07,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:44:07,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference/checkm_data
[2023-06-05 02:44:07,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:44:07,436] [INFO] Task started: CheckM
[2023-06-05 02:44:07,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/checkm_input GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/checkm_result
[2023-06-05 02:44:30,338] [INFO] Task succeeded: CheckM
[2023-06-05 02:44:30,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:44:30,359] [INFO] ===== Completeness check finished =====
[2023-06-05 02:44:30,359] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:44:30,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/markers.fasta)
[2023-06-05 02:44:30,360] [INFO] Task started: Blastn
[2023-06-05 02:44:30,360] [INFO] Running command: blastn -query GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/markers.fasta -db /var/lib/cwl/stg796bdc2e-2e60-4cb8-80bd-fab21a5d8c94/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:44:31,314] [INFO] Task succeeded: Blastn
[2023-06-05 02:44:31,319] [INFO] Selected 14 target genomes.
[2023-06-05 02:44:31,320] [INFO] Target genome list was writen to GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:44:31,353] [INFO] Task started: fastANI
[2023-06-05 02:44:31,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgc22e0104-5dd3-465d-9f73-16013346176a/GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna.gz --refList GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/target_genomes_gtdb.txt --output GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:44:37,714] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:37,733] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:44:37,733] [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_900315925.1	s__Succiniclasticum sp900315925	96.3172	554	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	96.41	95.14	0.84	0.70	42	conclusive
GCF_900112895.1	s__Succiniclasticum ruminis	86.3802	457	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801365.1	s__Succiniclasticum sp902801365	86.3653	421	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.72	97.62	0.82	0.80	3	-
GCA_017405945.1	s__Succiniclasticum sp017405945	86.1748	455	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443165.1	s__Succiniclasticum sp017443165	84.8306	235	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233365.1	s__Succiniclasticum sp905233365	84.5151	410	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	98.76	98.76	0.84	0.84	2	-
GCA_003512125.1	s__Succiniclasticum sp003512125	83.1156	267	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	98.84	98.84	0.85	0.85	2	-
GCA_017554485.1	s__Succiniclasticum sp017554485	82.2974	398	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342505.1	s__Succiniclasticum sp002342505	80.7257	283	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.62	97.51	0.81	0.72	6	-
GCA_900315345.1	s__Succiniclasticum sp900315345	80.6394	352	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.51	96.16	0.86	0.76	12	-
GCA_017460905.1	s__Succiniclasticum sp017460905	80.6387	273	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.67	97.67	0.73	0.73	2	-
GCA_900315805.1	s__Succiniclasticum sp900315805	77.9148	111	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	99.92	99.83	0.97	0.96	5	-
GCA_900316935.1	s__Succiniclasticum sp900316935	77.2921	100	667	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	99.76	99.29	0.95	0.93	11	-
--------------------------------------------------------------------------------
[2023-06-05 02:44:37,735] [INFO] GTDB search result was written to GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/result_gtdb.tsv
[2023-06-05 02:44:37,736] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:44:37,739] [INFO] DFAST_QC result json was written to GCA_902782355.1_Rumen_uncultured_genome_RUG12756_genomic.fna/dqc_result.json
[2023-06-05 02:44:37,739] [INFO] DFAST_QC completed!
[2023-06-05 02:44:37,739] [INFO] Total running time: 0h0m50s