[2023-06-18 22:32:44,525] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:32:44,529] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:32:44,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference
[2023-06-18 22:32:45,787] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:32:45,787] [INFO] Task started: Prodigal
[2023-06-18 22:32:45,788] [INFO] Running command: gunzip -c /var/lib/cwl/stgca4da511-962a-4eab-a4de-f4de6d8682c7/GCA_018883025.1_ASM1888302v1_genomic.fna.gz | prodigal -d GCA_018883025.1_ASM1888302v1_genomic.fna/cds.fna -a GCA_018883025.1_ASM1888302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:32:48,915] [INFO] Task succeeded: Prodigal
[2023-06-18 22:32:48,916] [INFO] Task started: HMMsearch
[2023-06-18 22:32:48,916] [INFO] Running command: hmmsearch --tblout GCA_018883025.1_ASM1888302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference/reference_markers.hmm GCA_018883025.1_ASM1888302v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:32:49,140] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:32:49,141] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgca4da511-962a-4eab-a4de-f4de6d8682c7/GCA_018883025.1_ASM1888302v1_genomic.fna.gz]
[2023-06-18 22:32:49,168] [INFO] Query marker FASTA was written to GCA_018883025.1_ASM1888302v1_genomic.fna/markers.fasta
[2023-06-18 22:32:49,169] [INFO] Task started: Blastn
[2023-06-18 22:32:49,169] [INFO] Running command: blastn -query GCA_018883025.1_ASM1888302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference/reference_markers.fasta -out GCA_018883025.1_ASM1888302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:32:51,182] [INFO] Task succeeded: Blastn
[2023-06-18 22:32:51,191] [INFO] Selected 22 target genomes.
[2023-06-18 22:32:51,191] [INFO] Target genome list was writen to GCA_018883025.1_ASM1888302v1_genomic.fna/target_genomes.txt
[2023-06-18 22:32:51,194] [INFO] Task started: fastANI
[2023-06-18 22:32:51,195] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4da511-962a-4eab-a4de-f4de6d8682c7/GCA_018883025.1_ASM1888302v1_genomic.fna.gz --refList GCA_018883025.1_ASM1888302v1_genomic.fna/target_genomes.txt --output GCA_018883025.1_ASM1888302v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:33:11,268] [INFO] Task succeeded: fastANI
[2023-06-18 22:33:11,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:33:11,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:33:11,275] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:33:11,276] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:33:11,276] [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
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	76.8321	72	421	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.5353	88	421	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	76.534	110	421	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	76.4751	89	421	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	76.36	76	421	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.1371	55	421	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:33:11,278] [INFO] DFAST Taxonomy check result was written to GCA_018883025.1_ASM1888302v1_genomic.fna/tc_result.tsv
[2023-06-18 22:33:11,280] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:33:11,280] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:33:11,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference/checkm_data
[2023-06-18 22:33:11,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:33:11,306] [INFO] Task started: CheckM
[2023-06-18 22:33:11,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018883025.1_ASM1888302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018883025.1_ASM1888302v1_genomic.fna/checkm_input GCA_018883025.1_ASM1888302v1_genomic.fna/checkm_result
[2023-06-18 22:33:28,757] [INFO] Task succeeded: CheckM
[2023-06-18 22:33:28,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 22:33:28,795] [INFO] ===== Completeness check finished =====
[2023-06-18 22:33:28,795] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:33:28,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018883025.1_ASM1888302v1_genomic.fna/markers.fasta)
[2023-06-18 22:33:28,796] [INFO] Task started: Blastn
[2023-06-18 22:33:28,796] [INFO] Running command: blastn -query GCA_018883025.1_ASM1888302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35699a94-ed25-47a9-929d-bfe973c81ed7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018883025.1_ASM1888302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:33:29,743] [INFO] Task succeeded: Blastn
[2023-06-18 22:33:29,751] [INFO] Selected 14 target genomes.
[2023-06-18 22:33:29,752] [INFO] Target genome list was writen to GCA_018883025.1_ASM1888302v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:33:29,778] [INFO] Task started: fastANI
[2023-06-18 22:33:29,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4da511-962a-4eab-a4de-f4de6d8682c7/GCA_018883025.1_ASM1888302v1_genomic.fna.gz --refList GCA_018883025.1_ASM1888302v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018883025.1_ASM1888302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:33:36,470] [INFO] Task succeeded: fastANI
[2023-06-18 22:33:36,483] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:33:36,483] [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_018883025.1	s__67-14 sp018883025	100.0	417	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903891285.1	s__67-14 sp903891285	94.4627	319	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.08	99.08	0.89	0.89	2	-
GCA_903939845.1	s__67-14 sp903939845	79.326	235	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.80	99.74	0.97	0.96	7	-
GCA_017304845.1	s__67-14 sp017304845	78.7788	143	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897355.1	s__67-14 sp001897355	78.4988	209	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.98	99.98	0.99	0.99	2	-
GCA_016650125.1	s__67-14 sp016650125	78.1493	173	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649615.1	s__67-14 sp016649615	77.8873	162	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712175.1	s__67-14 sp016712175	77.7154	153	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933815.1	s__67-14 sp903933815	77.6441	138	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.48	99.43	0.90	0.88	5	-
GCA_016649905.1	s__VAYN01 sp016649905	77.346	141	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__VAYN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268415.1	s__VAYN01 sp018268415	77.2695	131	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__VAYN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268655.1	s__VAYN01 sp018268655	77.214	113	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__VAYN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268575.1	s__VAYN01 sp018268575	77.1862	136	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__VAYN01	95.0	96.22	96.22	0.76	0.76	2	-
GCA_018268675.1	s__VAYN01 sp018268675	77.1124	139	421	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__VAYN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:33:36,485] [INFO] GTDB search result was written to GCA_018883025.1_ASM1888302v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:33:36,490] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:33:36,496] [INFO] DFAST_QC result json was written to GCA_018883025.1_ASM1888302v1_genomic.fna/dqc_result.json
[2023-06-18 22:33:36,497] [INFO] DFAST_QC completed!
[2023-06-18 22:33:36,497] [INFO] Total running time: 0h0m52s