[2023-06-19 15:25:43,383] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:25:43,385] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:25:43,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference
[2023-06-19 15:25:44,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:25:44,833] [INFO] Task started: Prodigal
[2023-06-19 15:25:44,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgb85390db-7e9f-4746-b664-9072f48b0e57/GCA_013698015.1_ASM1369801v1_genomic.fna.gz | prodigal -d GCA_013698015.1_ASM1369801v1_genomic.fna/cds.fna -a GCA_013698015.1_ASM1369801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:25:51,021] [INFO] Task succeeded: Prodigal
[2023-06-19 15:25:51,021] [INFO] Task started: HMMsearch
[2023-06-19 15:25:51,021] [INFO] Running command: hmmsearch --tblout GCA_013698015.1_ASM1369801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference/reference_markers.hmm GCA_013698015.1_ASM1369801v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:25:51,268] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:25:51,269] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb85390db-7e9f-4746-b664-9072f48b0e57/GCA_013698015.1_ASM1369801v1_genomic.fna.gz]
[2023-06-19 15:25:51,324] [INFO] Query marker FASTA was written to GCA_013698015.1_ASM1369801v1_genomic.fna/markers.fasta
[2023-06-19 15:25:51,325] [INFO] Task started: Blastn
[2023-06-19 15:25:51,325] [INFO] Running command: blastn -query GCA_013698015.1_ASM1369801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference/reference_markers.fasta -out GCA_013698015.1_ASM1369801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:25:51,956] [INFO] Task succeeded: Blastn
[2023-06-19 15:25:51,961] [INFO] Selected 12 target genomes.
[2023-06-19 15:25:51,961] [INFO] Target genome list was writen to GCA_013698015.1_ASM1369801v1_genomic.fna/target_genomes.txt
[2023-06-19 15:25:51,965] [INFO] Task started: fastANI
[2023-06-19 15:25:51,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgb85390db-7e9f-4746-b664-9072f48b0e57/GCA_013698015.1_ASM1369801v1_genomic.fna.gz --refList GCA_013698015.1_ASM1369801v1_genomic.fna/target_genomes.txt --output GCA_013698015.1_ASM1369801v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:26:00,332] [INFO] Task succeeded: fastANI
[2023-06-19 15:26:00,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:26:00,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:26:00,339] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 15:26:00,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 15:26:00,339] [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	78.0672	149	445	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	77.6998	98	445	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	76.9787	58	445	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	76.6775	69	445	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 15:26:00,342] [INFO] DFAST Taxonomy check result was written to GCA_013698015.1_ASM1369801v1_genomic.fna/tc_result.tsv
[2023-06-19 15:26:00,342] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:26:00,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:26:00,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference/checkm_data
[2023-06-19 15:26:00,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:26:00,380] [INFO] Task started: CheckM
[2023-06-19 15:26:00,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013698015.1_ASM1369801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013698015.1_ASM1369801v1_genomic.fna/checkm_input GCA_013698015.1_ASM1369801v1_genomic.fna/checkm_result
[2023-06-19 15:26:25,945] [INFO] Task succeeded: CheckM
[2023-06-19 15:26:25,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.69%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 15:26:25,984] [INFO] ===== Completeness check finished =====
[2023-06-19 15:26:25,984] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:26:25,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013698015.1_ASM1369801v1_genomic.fna/markers.fasta)
[2023-06-19 15:26:25,985] [INFO] Task started: Blastn
[2023-06-19 15:26:25,985] [INFO] Running command: blastn -query GCA_013698015.1_ASM1369801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0ca48a-bf84-4f05-9042-34c5f9392bb2/dqc_reference/reference_markers_gtdb.fasta -out GCA_013698015.1_ASM1369801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:26:26,808] [INFO] Task succeeded: Blastn
[2023-06-19 15:26:26,812] [INFO] Selected 8 target genomes.
[2023-06-19 15:26:26,812] [INFO] Target genome list was writen to GCA_013698015.1_ASM1369801v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:26:26,819] [INFO] Task started: fastANI
[2023-06-19 15:26:26,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgb85390db-7e9f-4746-b664-9072f48b0e57/GCA_013698015.1_ASM1369801v1_genomic.fna.gz --refList GCA_013698015.1_ASM1369801v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013698015.1_ASM1369801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:26:31,166] [INFO] Task succeeded: fastANI
[2023-06-19 15:26:31,179] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 15:26:31,179] [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_902806095.1	s__SCSIO-52909 sp902806095	80.9914	242	445	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_902812425.1	s__SCSIO-52909 sp902812425	80.6781	211	445	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	80.6652	166	445	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_016781725.1	s__SCSIO-52909 sp016781725	79.2458	122	445	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCA_902806085.1	s__SCSIO-52909 sp902806085	78.2817	161	445	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_011492945.1	s__SCSIO-52909 sp011492945	78.0672	149	445	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_902806015.1	s__SCSIO-52909 sp902806015	77.8573	113	445	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_902806075.1	s__SCSIO-52915 sp902806075	77.3051	57	445	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:26:31,182] [INFO] GTDB search result was written to GCA_013698015.1_ASM1369801v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:26:31,182] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:26:31,185] [INFO] DFAST_QC result json was written to GCA_013698015.1_ASM1369801v1_genomic.fna/dqc_result.json
[2023-06-19 15:26:31,185] [INFO] DFAST_QC completed!
[2023-06-19 15:26:31,185] [INFO] Total running time: 0h0m48s