[2023-06-16 22:23:38,099] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:23:38,102] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:23:38,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference
[2023-06-16 22:23:39,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:23:39,399] [INFO] Task started: Prodigal
[2023-06-16 22:23:39,399] [INFO] Running command: gunzip -c /var/lib/cwl/stg37e18302-ddd9-4e6f-8cd4-247570f198ed/GCA_003162855.1_20120800_S3X_genomic.fna.gz | prodigal -d GCA_003162855.1_20120800_S3X_genomic.fna/cds.fna -a GCA_003162855.1_20120800_S3X_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:23:47,717] [INFO] Task succeeded: Prodigal
[2023-06-16 22:23:47,718] [INFO] Task started: HMMsearch
[2023-06-16 22:23:47,718] [INFO] Running command: hmmsearch --tblout GCA_003162855.1_20120800_S3X_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference/reference_markers.hmm GCA_003162855.1_20120800_S3X_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:23:47,974] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:23:47,975] [INFO] Found 6/6 markers.
[2023-06-16 22:23:48,004] [INFO] Query marker FASTA was written to GCA_003162855.1_20120800_S3X_genomic.fna/markers.fasta
[2023-06-16 22:23:48,004] [INFO] Task started: Blastn
[2023-06-16 22:23:48,004] [INFO] Running command: blastn -query GCA_003162855.1_20120800_S3X_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference/reference_markers.fasta -out GCA_003162855.1_20120800_S3X_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:23:48,748] [INFO] Task succeeded: Blastn
[2023-06-16 22:23:48,752] [INFO] Selected 13 target genomes.
[2023-06-16 22:23:48,752] [INFO] Target genome list was writen to GCA_003162855.1_20120800_S3X_genomic.fna/target_genomes.txt
[2023-06-16 22:23:48,779] [INFO] Task started: fastANI
[2023-06-16 22:23:48,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg37e18302-ddd9-4e6f-8cd4-247570f198ed/GCA_003162855.1_20120800_S3X_genomic.fna.gz --refList GCA_003162855.1_20120800_S3X_genomic.fna/target_genomes.txt --output GCA_003162855.1_20120800_S3X_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:24:00,645] [INFO] Task succeeded: fastANI
[2023-06-16 22:24:00,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:24:00,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:24:00,656] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:24:00,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 22:24:00,657] [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
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	78.5922	342	946	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	78.2294	269	946	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	78.2175	228	946	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.0353	153	946	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.8875	203	946	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.8415	191	946	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.6793	166	946	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	77.4703	155	946	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.441	236	946	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.4199	192	946	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.8945	104	946	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.6853	120	946	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.6818	119	946	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:24:00,659] [INFO] DFAST Taxonomy check result was written to GCA_003162855.1_20120800_S3X_genomic.fna/tc_result.tsv
[2023-06-16 22:24:00,660] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:24:00,660] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:24:00,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference/checkm_data
[2023-06-16 22:24:00,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:24:00,703] [INFO] Task started: CheckM
[2023-06-16 22:24:00,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003162855.1_20120800_S3X_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003162855.1_20120800_S3X_genomic.fna/checkm_input GCA_003162855.1_20120800_S3X_genomic.fna/checkm_result
[2023-06-16 22:24:29,651] [INFO] Task succeeded: CheckM
[2023-06-16 22:24:29,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:24:29,679] [INFO] ===== Completeness check finished =====
[2023-06-16 22:24:29,679] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:24:29,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003162855.1_20120800_S3X_genomic.fna/markers.fasta)
[2023-06-16 22:24:29,680] [INFO] Task started: Blastn
[2023-06-16 22:24:29,680] [INFO] Running command: blastn -query GCA_003162855.1_20120800_S3X_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df9da34-b08c-4d77-b39b-709a7829e7de/dqc_reference/reference_markers_gtdb.fasta -out GCA_003162855.1_20120800_S3X_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:24:30,736] [INFO] Task succeeded: Blastn
[2023-06-16 22:24:30,743] [INFO] Selected 15 target genomes.
[2023-06-16 22:24:30,744] [INFO] Target genome list was writen to GCA_003162855.1_20120800_S3X_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:24:30,783] [INFO] Task started: fastANI
[2023-06-16 22:24:30,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg37e18302-ddd9-4e6f-8cd4-247570f198ed/GCA_003162855.1_20120800_S3X_genomic.fna.gz --refList GCA_003162855.1_20120800_S3X_genomic.fna/target_genomes_gtdb.txt --output GCA_003162855.1_20120800_S3X_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:24:43,313] [INFO] Task succeeded: fastANI
[2023-06-16 22:24:43,326] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:24:43,327] [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_003138795.1	s__UBA5172 sp003138795	99.8049	847	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	99.74	99.67	0.90	0.89	6	conclusive
GCF_009765785.1	s__UBA5172 sp009765785	80.7737	499	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083945.1	s__UBA5172 sp014083945	79.5264	345	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203225.1	s__Granulicella_A mallensis_A	78.7615	334	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766105.1	s__Granulicella_A sp009766105	78.6197	304	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178955.2	s__Granulicella_A mallensis	78.5922	342	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873705.1	s__CAIQPK01 sp903873705	78.4804	278	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCA_003132145.1	s__Palsa-288 sp003132145	78.3425	192	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.75	99.72	0.90	0.88	3	-
GCF_900108185.1	s__Bryocella elongata	78.2218	269	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Bryocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	78.2015	229	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268895.1	s__Edaphobacter sp018268895	77.8748	185	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142215.1	s__Palsa-288 sp003142215	77.7957	178	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.59	99.59	0.84	0.84	2	-
GCA_003142235.1	s__Palsa-288 sp003142235	77.7623	171	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.72	99.67	0.90	0.89	3	-
GCF_900188085.1	s__Granulicella_C rosea	77.441	236	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131625.1	s__Palsa-343 sp003131625	76.043	98	946	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:24:43,329] [INFO] GTDB search result was written to GCA_003162855.1_20120800_S3X_genomic.fna/result_gtdb.tsv
[2023-06-16 22:24:43,330] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:24:43,334] [INFO] DFAST_QC result json was written to GCA_003162855.1_20120800_S3X_genomic.fna/dqc_result.json
[2023-06-16 22:24:43,334] [INFO] DFAST_QC completed!
[2023-06-16 22:24:43,334] [INFO] Total running time: 0h1m5s