[2023-06-29 23:40:54,284] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:40:54,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:40:54,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference
[2023-06-29 23:40:55,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:40:55,578] [INFO] Task started: Prodigal
[2023-06-29 23:40:55,579] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd9b96a9-9b04-47e0-8f97-72910f2ae17f/GCA_016781855.1_ASM1678185v1_genomic.fna.gz | prodigal -d GCA_016781855.1_ASM1678185v1_genomic.fna/cds.fna -a GCA_016781855.1_ASM1678185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:41:01,101] [INFO] Task succeeded: Prodigal
[2023-06-29 23:41:01,102] [INFO] Task started: HMMsearch
[2023-06-29 23:41:01,102] [INFO] Running command: hmmsearch --tblout GCA_016781855.1_ASM1678185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference/reference_markers.hmm GCA_016781855.1_ASM1678185v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:41:01,338] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:41:01,339] [INFO] Found 6/6 markers.
[2023-06-29 23:41:01,364] [INFO] Query marker FASTA was written to GCA_016781855.1_ASM1678185v1_genomic.fna/markers.fasta
[2023-06-29 23:41:01,364] [INFO] Task started: Blastn
[2023-06-29 23:41:01,364] [INFO] Running command: blastn -query GCA_016781855.1_ASM1678185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference/reference_markers.fasta -out GCA_016781855.1_ASM1678185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:41:01,988] [INFO] Task succeeded: Blastn
[2023-06-29 23:41:01,993] [INFO] Selected 16 target genomes.
[2023-06-29 23:41:01,993] [INFO] Target genome list was writen to GCA_016781855.1_ASM1678185v1_genomic.fna/target_genomes.txt
[2023-06-29 23:41:01,995] [INFO] Task started: fastANI
[2023-06-29 23:41:01,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd9b96a9-9b04-47e0-8f97-72910f2ae17f/GCA_016781855.1_ASM1678185v1_genomic.fna.gz --refList GCA_016781855.1_ASM1678185v1_genomic.fna/target_genomes.txt --output GCA_016781855.1_ASM1678185v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:41:13,955] [INFO] Task succeeded: fastANI
[2023-06-29 23:41:13,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:41:13,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:41:13,970] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:41:13,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:41:13,971] [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
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	79.8926	303	491	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	78.9058	245	491	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.4013	155	491	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.2933	148	491	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	77.2506	106	491	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.2779	59	491	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	74.8482	55	491	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	74.8414	51	491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:41:13,973] [INFO] DFAST Taxonomy check result was written to GCA_016781855.1_ASM1678185v1_genomic.fna/tc_result.tsv
[2023-06-29 23:41:13,973] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:41:13,973] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:41:13,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference/checkm_data
[2023-06-29 23:41:13,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:41:14,011] [INFO] Task started: CheckM
[2023-06-29 23:41:14,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016781855.1_ASM1678185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016781855.1_ASM1678185v1_genomic.fna/checkm_input GCA_016781855.1_ASM1678185v1_genomic.fna/checkm_result
[2023-06-29 23:41:36,656] [INFO] Task succeeded: CheckM
[2023-06-29 23:41:36,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.16%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 23:41:36,683] [INFO] ===== Completeness check finished =====
[2023-06-29 23:41:36,684] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:41:36,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016781855.1_ASM1678185v1_genomic.fna/markers.fasta)
[2023-06-29 23:41:36,685] [INFO] Task started: Blastn
[2023-06-29 23:41:36,685] [INFO] Running command: blastn -query GCA_016781855.1_ASM1678185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b26f038-941b-4947-a49f-179c45355044/dqc_reference/reference_markers_gtdb.fasta -out GCA_016781855.1_ASM1678185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:41:37,515] [INFO] Task succeeded: Blastn
[2023-06-29 23:41:37,521] [INFO] Selected 14 target genomes.
[2023-06-29 23:41:37,521] [INFO] Target genome list was writen to GCA_016781855.1_ASM1678185v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:41:37,546] [INFO] Task started: fastANI
[2023-06-29 23:41:37,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd9b96a9-9b04-47e0-8f97-72910f2ae17f/GCA_016781855.1_ASM1678185v1_genomic.fna.gz --refList GCA_016781855.1_ASM1678185v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016781855.1_ASM1678185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:41:46,207] [INFO] Task succeeded: fastANI
[2023-06-29 23:41:46,223] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:41:46,223] [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_016781725.1	s__SCSIO-52909 sp016781725	98.7849	361	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	conclusive
GCA_902812425.1	s__SCSIO-52909 sp902812425	81.2252	273	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806085.1	s__SCSIO-52909 sp902806085	80.3183	307	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806095.1	s__SCSIO-52909 sp902806095	80.2938	270	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805975.1	s__SCSIO-52909 sp902805975	80.1507	254	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815575.1	s__SCSIO-52909 sp013815575	79.9156	191	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	97.69	97.69	0.64	0.64	2	-
GCF_011492945.1	s__SCSIO-52909 sp011492945	79.8926	303	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805985.1	s__SCSIO-52909 sp902805985	79.8374	221	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698525.1	s__SCSIO-52909 sp013698525	79.8204	178	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011492965.1	s__SCSIO-52915 sp011492965	78.9057	245	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695335.1	s__JACDGB01 sp013695335	78.083	147	491	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACDGB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:41:46,225] [INFO] GTDB search result was written to GCA_016781855.1_ASM1678185v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:41:46,225] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:41:46,229] [INFO] DFAST_QC result json was written to GCA_016781855.1_ASM1678185v1_genomic.fna/dqc_result.json
[2023-06-29 23:41:46,229] [INFO] DFAST_QC completed!
[2023-06-29 23:41:46,229] [INFO] Total running time: 0h0m52s