[2023-06-28 12:01:01,886] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:01:01,888] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:01:01,888] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference
[2023-06-28 12:01:03,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:01:03,362] [INFO] Task started: Prodigal
[2023-06-28 12:01:03,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg48918652-a08f-4d05-9ed1-cab222e771fa/GCA_012269405.1_ASM1226940v1_genomic.fna.gz | prodigal -d GCA_012269405.1_ASM1226940v1_genomic.fna/cds.fna -a GCA_012269405.1_ASM1226940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:01:09,591] [INFO] Task succeeded: Prodigal
[2023-06-28 12:01:09,592] [INFO] Task started: HMMsearch
[2023-06-28 12:01:09,592] [INFO] Running command: hmmsearch --tblout GCA_012269405.1_ASM1226940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference/reference_markers.hmm GCA_012269405.1_ASM1226940v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:01:09,842] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:01:09,843] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48918652-a08f-4d05-9ed1-cab222e771fa/GCA_012269405.1_ASM1226940v1_genomic.fna.gz]
[2023-06-28 12:01:09,882] [INFO] Query marker FASTA was written to GCA_012269405.1_ASM1226940v1_genomic.fna/markers.fasta
[2023-06-28 12:01:09,883] [INFO] Task started: Blastn
[2023-06-28 12:01:09,883] [INFO] Running command: blastn -query GCA_012269405.1_ASM1226940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference/reference_markers.fasta -out GCA_012269405.1_ASM1226940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:10,515] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:10,520] [INFO] Selected 25 target genomes.
[2023-06-28 12:01:10,521] [INFO] Target genome list was writen to GCA_012269405.1_ASM1226940v1_genomic.fna/target_genomes.txt
[2023-06-28 12:01:10,524] [INFO] Task started: fastANI
[2023-06-28 12:01:10,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg48918652-a08f-4d05-9ed1-cab222e771fa/GCA_012269405.1_ASM1226940v1_genomic.fna.gz --refList GCA_012269405.1_ASM1226940v1_genomic.fna/target_genomes.txt --output GCA_012269405.1_ASM1226940v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:01:27,137] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:27,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:01:27,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:01:27,141] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:01:27,141] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:01:27,141] [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
--------------------------------------------------------------------------------
[2023-06-28 12:01:27,144] [INFO] DFAST Taxonomy check result was written to GCA_012269405.1_ASM1226940v1_genomic.fna/tc_result.tsv
[2023-06-28 12:01:27,144] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:01:27,145] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:01:27,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference/checkm_data
[2023-06-28 12:01:27,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:01:27,180] [INFO] Task started: CheckM
[2023-06-28 12:01:27,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012269405.1_ASM1226940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012269405.1_ASM1226940v1_genomic.fna/checkm_input GCA_012269405.1_ASM1226940v1_genomic.fna/checkm_result
[2023-06-28 12:01:52,122] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:52,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:01:52,146] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:52,146] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:52,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012269405.1_ASM1226940v1_genomic.fna/markers.fasta)
[2023-06-28 12:01:52,147] [INFO] Task started: Blastn
[2023-06-28 12:01:52,147] [INFO] Running command: blastn -query GCA_012269405.1_ASM1226940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf32dc4a-ef15-4711-b54d-e92c6da29329/dqc_reference/reference_markers_gtdb.fasta -out GCA_012269405.1_ASM1226940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:53,051] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:53,056] [INFO] Selected 8 target genomes.
[2023-06-28 12:01:53,056] [INFO] Target genome list was writen to GCA_012269405.1_ASM1226940v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:53,058] [INFO] Task started: fastANI
[2023-06-28 12:01:53,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg48918652-a08f-4d05-9ed1-cab222e771fa/GCA_012269405.1_ASM1226940v1_genomic.fna.gz --refList GCA_012269405.1_ASM1226940v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012269405.1_ASM1226940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:57,443] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:57,453] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:01:57,453] [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_008081045.1	s__UBA9145 sp008081045	98.6514	615	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.92	98.40	0.89	0.82	4	conclusive
GCA_902537815.1	s__UBA9145 sp902537815	94.7249	417	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597095.1	s__UBA9145 sp902597095	94.2905	464	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691885.1	s__UBA9145 sp002691885	87.4054	463	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002729315.1	s__UBA9145 sp002729315	86.795	484	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719575.1	s__UBA9145 sp002719575	79.3187	284	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477465.1	s__UBA9145 sp002477465	76.8065	108	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
--------------------------------------------------------------------------------
[2023-06-28 12:01:57,455] [INFO] GTDB search result was written to GCA_012269405.1_ASM1226940v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:57,456] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:57,458] [INFO] DFAST_QC result json was written to GCA_012269405.1_ASM1226940v1_genomic.fna/dqc_result.json
[2023-06-28 12:01:57,459] [INFO] DFAST_QC completed!
[2023-06-28 12:01:57,459] [INFO] Total running time: 0h0m56s